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Microorganisms
Volume 6
Issue 4
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Microorganisms, Volume 6, Issue 4 (December 2018) – 33 articles

Cover Story (view full-size image): STEC is a foodborne pathogen transmitted mainly by undercooked meat, contaminated fruits, vegetables, and water, but also the person to person route has been recently highlighted. Shiga toxin (Stx) is the main virulence factor of STEC and is responsible for developing a systemic complication known as Hemolytic Uremic Syndrome (HUS), characterized by hemolytic anemia thrombocytopenia and acute renal failure. STEC can produce Stx type 1 and/or 2 (Stx1, Stx2) and their variants, with Stx2 being more frequently associated with severe cases of HUS. Some experimental data suggest that Stx2 may impair pregnancy. We have proposed that symptomatic or asymptomatic STEC infections during early or late human pregnancy may cause maternal or fetal damage mediated by Stx2. In this article, we provide a brief overview of Stx2 action on placental tissues and discuss whether they might cause pregnancy loss or preterm [...] Read more.
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22 pages, 1977 KiB  
Review
Distinctive Nuclear Features of Dinoflagellates with A Particular Focus on Histone and Histone-Replacement Proteins
by Sadaf Riaz, Zhenghong Sui, Zeeshan Niaz, Sohrab Khan, Yuan Liu and Haoxin Liu
Microorganisms 2018, 6(4), 128; https://doi.org/10.3390/microorganisms6040128 - 14 Dec 2018
Cited by 15 | Viewed by 5935
Abstract
Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates “dinokaryon” have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed [...] Read more.
Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates “dinokaryon” have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed nucleosome-less chromatin, immense genome, low protein to DNA ratio, guanine-cytosine rich methylated DNA, and unique mitosis process. Furthermore, dinoflagellates are the only known group of eukaryotes that apparently lack histone proteins. Over the course of evolution, dinoflagellates have recruited other proteins, e.g., histone-like proteins (HLPs), from bacteria and dinoflagellates/viral nucleoproteins (DVNPs) from viruses as histone substitutes. Expression diversity of these nucleoproteins has greatly influenced the chromatin structure and gene expression regulation in dinoflagellates. Histone replacement proteins (HLPs and DVNPs) are hypothesized to perform a few similar roles as histone proteins do in other eukaryotes, i.e., gene expression regulation and repairing DNA. However, their role in bulk packaging of DNA is not significant as low amounts of proteins are associated with the gigantic genome. This review intends to summarize the discoveries encompassing unique nuclear features of dinoflagellates, particularly focusing on histone and histone replacement proteins. In addition, a comprehensive view of the evolution of dinoflagellate nuclei is presented. Full article
(This article belongs to the Special Issue Dinoflagellate Biology in the Omics Era)
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17 pages, 1566 KiB  
Article
Membrane and Cytoplasmic Proteins of Mycobacterium avium subspecies paratuberculosis that Bind to Novel Monoclonal Antibodies
by John P. Bannantine, Judith R. Stabel, John D. Lippolis and Timothy A. Reinhardt
Microorganisms 2018, 6(4), 127; https://doi.org/10.3390/microorganisms6040127 - 11 Dec 2018
Cited by 6 | Viewed by 5055
Abstract
Monoclonal antibodies against Mycobacterium avium subspecies paratuberculosis (Map) proteins are important tools in Johne’s disease research and diagnostics. Johne’s disease is a chronic inflammatory intestinal disease of cattle, sheep, and other ruminant animals. We have previously generated multiple sets of monoclonal antibodies (mAbs) [...] Read more.
Monoclonal antibodies against Mycobacterium avium subspecies paratuberculosis (Map) proteins are important tools in Johne’s disease research and diagnostics. Johne’s disease is a chronic inflammatory intestinal disease of cattle, sheep, and other ruminant animals. We have previously generated multiple sets of monoclonal antibodies (mAbs) in different studies; however, because many were generated and screened against a whole-cell extract of Map, the antigens that bind to these antibodies remained unknown. In this study, we used three different approaches to identify the corresponding Map antigens for 14 mAbs that could not be identified previously. In the first approach, a new Map-lambda phage expression library was screened to identify corresponding antigens for 11 mAbs. This approach revealed that mAbs 7C8, 9H3, 12E4, 3G5, and 11B8 all detect MAP_3404 encoding the biotin carboxylase subunit of acetyl-CoA carboxylase, while mAbs 7A6, 11F8, and 10C12 detect the GroEL2 chaperonin (MAP_3936), 6C9 detects electron transfer flavoprotein (MAP_3060c), and 14G11 detects MAP_3976, a lipoprotein anchoring transpeptidase. The epitopes to a selection of these mAbs were also defined. In a second approach, MAP_2698c bound monoclonal antibody (mAb) 14D4 as determined using protein arrays. When both of these approaches failed to identify the antigen for mAb 12C9, immunoprecipitation, mass spectrometry analysis, and codon optimization was used to identify the membrane protein, MAP_4145, as the reacting antigen. Characterized antibodies were used to quickly interrogate mycobacterial proteomic preps. We conclude by providing a complete catalog of available mAbs to Map proteins, along with their cognate antigens and epitopes, if known. These antibodies are now thoroughly characterized and more useful for research and diagnostic purposes. Full article
(This article belongs to the Special Issue Virulence Identification and Analysis from Pathogenic Mycobacteria of Humans and Animals)
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12 pages, 242 KiB  
Article
Presence of Shiga Toxin-Producing Escherichia coli (STEC) in Fresh Beef Marketed in 13 Regions of ITALY (2017)
by Bianca Maria Varcasia, Francesco Tomassetti, Laura De Santis, Fabiola Di Giamberardino, Sarah Lovari, Stefano Bilei and Paola De Santis
Microorganisms 2018, 6(4), 126; https://doi.org/10.3390/microorganisms6040126 - 6 Dec 2018
Cited by 12 | Viewed by 4075
Abstract
The aim of this study was to determine the prevalence of Shiga toxin-producing Escherichia coli in fresh beef marketed in 2017 in 13 regions of Italy, to evaluate the potential risk to human health. According to the ISO/TS 13136:2012 standard, 239 samples were [...] Read more.
The aim of this study was to determine the prevalence of Shiga toxin-producing Escherichia coli in fresh beef marketed in 2017 in 13 regions of Italy, to evaluate the potential risk to human health. According to the ISO/TS 13136:2012 standard, 239 samples were analysed and nine were STEC positive, from which 20 strains were isolated. The STEC-positive samples were obtained from Calabria (n = 1), Campania (n = 1), Lazio (n = 2), Liguria (n = 1), Lombardia (n = 1) and Veneto (n = 3). All STEC strains were analysed for serogroups O26, O45, O55, O91, O103, O104, O111, O113, O121, O128, O145, O146 and O157, using Real-Time PCR. Three serogroups were identified amongst the 20 strains: O91 (n = 5), O113 (n = 2), and O157 (n = 1); the O-group for each of the 12 remaining STEC strains was not identified. Six stx subtypes were detected: stx1a, stx1c, stx2a, stx2b, stx2c and stx2d. Subtype stx2c was the most common, followed by stx2d and stx2b. Subtype stx2a was identified in only one eae-negative strain and occurred in combination with stx1a, stx1c and stx2b. The presence in meat of STEC strains being potentially harmful to human health shows the importance, during harvest, of implementing additional measures to reduce contamination risk. Full article
(This article belongs to the Special Issue Advances in Prevention of Foodborne Pathogens of Public Health Concern during Manufacturing)
20 pages, 2052 KiB  
Article
Sequential Combined Effect of Phages and Antibiotics on the Inactivation of Escherichia coli
by Ana Lopes, Carla Pereira and Adelaide Almeida
Microorganisms 2018, 6(4), 125; https://doi.org/10.3390/microorganisms6040125 - 5 Dec 2018
Cited by 49 | Viewed by 5212
Abstract
The emergence of antibiotic resistance in bacteria is a global concern. The use of bacteriophages (or phages) alone or combined with antibiotics is consolidating itself as an alternative approach to inactivate antibiotic-resistant bacteria. However, phage-resistant mutants have been considered as a major threat [...] Read more.
The emergence of antibiotic resistance in bacteria is a global concern. The use of bacteriophages (or phages) alone or combined with antibiotics is consolidating itself as an alternative approach to inactivate antibiotic-resistant bacteria. However, phage-resistant mutants have been considered as a major threat when phage treatment is employed. Escherichia coli is one of the main responsible pathogens for moderate and serious infections in hospital and community environments, being involved in the rapid evolution of fluoroquinolones and third-generation cephalosporin resistance. The aim of this study was to evaluate the effect of combined treatments of phages and antibiotics in the inactivation of E. coli. For this, ciprofloxacin at lethal and sublethal concentrations was added at different times (0, 6, 12 and 18 h) and was tested in combination with the phage ELY-1 to inactivate E. coli. The efficacy of the combined treatment varied with the antibiotic concentration and with the time of antibiotic addition. The combined treatment prevented bacterial regrowth when the antibiotic was used at minimum inhibitory concentration (MIC) and added after 6 h of phage addition, causing less bacterial resistance than phage and antibiotic applied alone (4.0 × 10−7 for the combined treatment, 3.9 × 10−6 and 3.4 × 10−5 for the antibiotics and the phages alone, respectively). Combined treatment with phage and antibiotic can be effective in reducing the bacterial density and it can also prevent the emergence of resistant variants. However, the antibiotic concentration and the time of antibiotic application are essential factors that need to be considered in the combined treatment. Full article
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16 pages, 1383 KiB  
Article
The Isolation and Identification of Bacteria on Feathers of Migratory Bird Species
by Antonella Giorgio, Salvatore De Bonis, Rosario Balestrieri, Giovanni Rossi and Marco Guida
Microorganisms 2018, 6(4), 124; https://doi.org/10.3390/microorganisms6040124 - 5 Dec 2018
Cited by 10 | Viewed by 5598
Abstract
Worldwide, bacteria are the most ubiquitous microorganisms, and it has been extensively demonstrated that migratory wild birds can increase bacterial global scale dispersion through long-distance migration and dispersal. The microbial community hosted by wild birds can be highly diverse, including pathogenic strains that [...] Read more.
Worldwide, bacteria are the most ubiquitous microorganisms, and it has been extensively demonstrated that migratory wild birds can increase bacterial global scale dispersion through long-distance migration and dispersal. The microbial community hosted by wild birds can be highly diverse, including pathogenic strains that can contribute to infections and disease spread. This study focused on feather and plumage bacteria within bird microbial communities. Samples were collected during ornithological activities in a bird ringing station. Bacterial identification was carried out via DNA barcoding of the partial 16S rRNA gene. Thirty-seven isolates of bacteria were identified on the chest feathers of 60 migratory birds belonging to three trans-Saharan species: Muscicapa striata, Hippolais icterina, and Sylvia borin. Our results demonstrate the possibility of bacterial transfer, including pathogens, through bird migration between very distant countries. The data from the analysis of plumage bacteria can aid in the explanation of phenomena such as migratory birds’ fitness or the development of secondary sexual traits. Moreover, these results have deep hygienic–sanitary implications, since many bird species have synanthropic behaviors during their migration that increase the probability of disease spread. Full article
(This article belongs to the Section Environmental Microbiology)
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11 pages, 1596 KiB  
Article
Combination of Posaconazole and Amphotericin B in the Treatment of Candida glabrata Biofilms
by Célia F. Rodrigues, Diana F. Alves and Mariana Henriques
Microorganisms 2018, 6(4), 123; https://doi.org/10.3390/microorganisms6040123 - 4 Dec 2018
Cited by 17 | Viewed by 4186
Abstract
Candidemia cases have been increasing, especially among immunosuppressed patients. Candida glabrata is one of the most resistant Candida species, especially to the azole drugs, resulting in a high demand for therapeutic alternatives. The minimum inhibitory concentration (MIC), minimum fungicidal concentration (MFC), and minimum [...] Read more.
Candidemia cases have been increasing, especially among immunosuppressed patients. Candida glabrata is one of the most resistant Candida species, especially to the azole drugs, resulting in a high demand for therapeutic alternatives. The minimum inhibitory concentration (MIC), minimum fungicidal concentration (MFC), and minimum biofilm eradication concentration (MBEC) were determined for posaconazole (Pcz) and amphotericin B (AmB). The drug combinations of both drugs were evaluated on pre-formed biofilms of C. glabrata ATCC 2001, through XTT (2,3-bis (2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide) assay, colony forming units (CFU), crystal violet, and the fractional inhibitory concentration index (FICI). C. glabrata revealed higher susceptibility and biofilm reduction in the presence of AmB alone, but both drugs revealed a good capacity in the biomass elimination. In the majority of the tested combinations, the interactions were defined as indifferent (FICI ≤ 4). The combination of the two drugs does not seem to bring a clear advantage in the treatment of biofilms of C. glabrata. Full article
(This article belongs to the Special Issue Strategies and Weapons to Fight Antimicrobial Resistance)
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11 pages, 471 KiB  
Article
Antimicrobial Activity of Several Cineole-Rich Western Australian Eucalyptus Essential Oils
by Fahad S. Aldoghaim, Gavin R. Flematti and Katherine A. Hammer
Microorganisms 2018, 6(4), 122; https://doi.org/10.3390/microorganisms6040122 - 3 Dec 2018
Cited by 46 | Viewed by 6008
Abstract
Essential oils from the Western Australian (WA) Eucalyptus mallee species Eucalyptus loxophleba, Eucalyptus polybractea, and Eucalyptus kochii subsp. plenissima and subsp. borealis were hydrodistilled from the leaves and then analysed by gas chromatography–mass spectrometry in addition to a commercial Eucalyptus globulus [...] Read more.
Essential oils from the Western Australian (WA) Eucalyptus mallee species Eucalyptus loxophleba, Eucalyptus polybractea, and Eucalyptus kochii subsp. plenissima and subsp. borealis were hydrodistilled from the leaves and then analysed by gas chromatography–mass spectrometry in addition to a commercial Eucalyptus globulus oil and 1,8-cineole. The main component of all oils was 1,8-cineole at 97.32% for E. kochii subsp. borealis, 96.55% for E. kochii subsp. plenissima, 82.95% for E. polybractea, 78.78% for E. loxophleba 2, 77.02% for E. globulus, and 66.93% for E. loxophleba 1. The Eucalyptus oils exhibited variable antimicrobial activity determined by broth microdilution, with E. globulus and E. polybractea oils showing the highest activities. The majority of microorganisms were inhibited or killed at concentrations ranging from 0.25% to 8.0% (v/v). Enterococcus faecalis and Candida albicans were the least susceptible organisms, whilst Acinetobacter baumannii was the most sensitive. In conclusion, all oils from WA Eucalyptus species showed microorganism inhibitory activity, although this varied according to both the Eucalyptus species and the microorganism tested. These data demonstrate that WA Eucalyptus oils show activity against a range of medically important pathogens and therefore have potential as antimicrobial agents. Full article
(This article belongs to the Section Medical Microbiology)
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17 pages, 1503 KiB  
Article
Application of A Novel Potential Probiotic Lactobacillus paracasei Strain Isolated from Kefir Grains in the Production of Feta-Type Cheese
by Ioanna Mantzourani, Antonia Terpou, Athanasios Alexopoulos, Pelagia Chondrou, Alex Galanis, Argyro Bekatorou, Eugenia Bezirtzoglou, Athanasios A Koutinas and Stavros Plessas
Microorganisms 2018, 6(4), 121; https://doi.org/10.3390/microorganisms6040121 - 29 Nov 2018
Cited by 17 | Viewed by 4629
Abstract
In the present study 38 lactic acid bacteria strains were isolated from kefir grains and were monitored regarding probiotic properties in a series of established in vitro tests, including resistance to low pH, resistance to pepsin and pancreatin, and tolerance to bile salts, [...] Read more.
In the present study 38 lactic acid bacteria strains were isolated from kefir grains and were monitored regarding probiotic properties in a series of established in vitro tests, including resistance to low pH, resistance to pepsin and pancreatin, and tolerance to bile salts, as well as susceptibility against common antibiotics. Among them, the strain SP3 displayed potential probiotic properties. Multiplex PCR analysis indicated that the novel strain belongs to the paracasei species. Likewise, the novel strain (Lactobacillus paracasei SP3) was applied as a starter culture for Feta-type cheese production. Feta-type cheese production resulted in significantly higher acidity; lower pH; reduced counts of coliforms, yeasts and fungi; and improved quality characteristics compared with cheese samples produced with no starter culture. Finally, it is highlighted that the application of the novel strain led to Feta-type cheese production with improved overall quality and sensory characteristics. Full article
(This article belongs to the Section Food Microbiology)
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3 pages, 741 KiB  
Editorial
Microorganisms 2018 Best Paper Award
by Microorganisms Editorial Office
Microorganisms 2018, 6(4), 120; https://doi.org/10.3390/microorganisms6040120 - 28 Nov 2018
Cited by 1 | Viewed by 2664
Abstract
Microorganisms is instituting an annual award to recognize the outstanding papers published in the journal. [...] Full article
18 pages, 1289 KiB  
Article
Assessing the Efficiency of Molecular Markers for the Species Identification of Gregarines Isolated from the Mealworm and Super Worm Midgut
by Chiara Nocciolini, Claudio Cucini, Chiara Leo, Valeria Francardi, Elena Dreassi and Antonio Carapelli
Microorganisms 2018, 6(4), 119; https://doi.org/10.3390/microorganisms6040119 - 27 Nov 2018
Cited by 5 | Viewed by 5332
Abstract
Protozoa, of the taxon Gregarinasina, are a heterogeneous group of Apicomplexa that includes ~1600 species. They are parasites of a large variety of both marine and terrestrial invertebrates, mainly annelids, arthropods and mollusks. Unlike coccidians and heamosporidians, gregarines have not proven to have [...] Read more.
Protozoa, of the taxon Gregarinasina, are a heterogeneous group of Apicomplexa that includes ~1600 species. They are parasites of a large variety of both marine and terrestrial invertebrates, mainly annelids, arthropods and mollusks. Unlike coccidians and heamosporidians, gregarines have not proven to have a negative effect on human welfare; thus, they have been poorly investigated. This study focuses on the molecular identification and phylogeny of the gregarine species found in the midgut of two insect species that are considered as an alternative source of animal proteins for the human diet: the mealworm Tenebrio molitor, and the super-worm Zophobas atratus (Coleoptera: Tenebrionidae). Gregarine specimens were isolated from the gut of both larval and adult stages of T. molitor specimens, as well as from Z. atratus larvae. The morphological analyses were restricted to the identification of the different parasite morpho-types, likely corresponding either to different life-cycle stages or to alternative gregarine species. The samples were also used for the DNA extraction necessary for their genetic characterization. Finally, the efficiency of different molecular markers (i.e., 18S rDNA gene alone or combined with the Internal Transcribed Spacer 1) was assessed when applied either to gregarine species identification and to phylogenetic inference. Full article
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15 pages, 1626 KiB  
Article
Low Concentration of Antibiotics Modulates Gut Microbiota at Different Levels in Pre-Weaning Dairy Calves
by Mohammed Husien Yousif, Jing-Hui Li, Zheng-Qian Li, Gibson Maswayi Alugongo, Shou-Kun Ji, Yuan-Xiao Li, Ya-Jing Wang, Sheng-Li Li and Zhi-Jun Cao
Microorganisms 2018, 6(4), 118; https://doi.org/10.3390/microorganisms6040118 - 27 Nov 2018
Cited by 19 | Viewed by 4464
Abstract
The aim of this study was to investigate the effect of feeding milk replacer (MR) with two different antibiotics treatments on the gut microbiota of pre-weaning calves. Twelve (12) Holstein male calves at 1-day-old were randomly assigned to: milk replacer without antibiotics (CON), [...] Read more.
The aim of this study was to investigate the effect of feeding milk replacer (MR) with two different antibiotics treatments on the gut microbiota of pre-weaning calves. Twelve (12) Holstein male calves at 1-day-old were randomly assigned to: milk replacer without antibiotics (CON), milk replacer plus low cocktail of antibiotics (LCA) concentration (penicillin 0.024 mg/L, streptomycin 0.025 mg/L, tetracycline 0.1 mg/L, ceftiofur 0.33 mg/L), and milk replacer plus a low concentration of single antibiotic (LSA; ceftiofur 0.33 mg/L). All the calves were harvested at 35-day-old, and the digesta from the ileum and colon was collected in addition to fecal samples. Samples were analyzed by 16S rRNA gene using Illumina MiSeq platform. Results showed that there were significant differences among treatments in the ileum, where LCA significantly reduced the relative abundance of Enterobacteriaceae (P = 0.02) especially Escherichia-coli (P = 0.02), while LSA significantly reduced the relative abundance of Comamonas (P = 0.02). In the colon and rectum, LSA treatment was significantly enriched with the class Bacilli, whereas the control group was significantly enriched with Alloprevotlla (P = 0.03). However, at the family level in the rectum LCA and LSA significantly reduced the relative abundance of Acidaminococcaceae (P = 0.01). Moreover, at the genera level in the colon, LSA significantly increased Prevotellaceae_Ga6A1_ group (P = 0.02), whereas in the rectum both of treatments reduced the relative abundance of Phascolarctobacterium (P = 0.01). In conclusion, the overall low cocktail of antibiotics concentration induced changes at different taxonomic levels; specifically the decrease in Escherichia-coli which might subsequently reduce the incidences of diarrhea in calves. Full article
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14 pages, 2931 KiB  
Article
Distribution and Antimicrobial Resistance of Salmonella Isolated from Pigs with Diarrhea in China
by Jin-Hui Su, Yao-Hong Zhu, Tian-Yi Ren, Liang Guo, Gui-Yan Yang, Lian-Guo Jiao and Jiu-Feng Wang
Microorganisms 2018, 6(4), 117; https://doi.org/10.3390/microorganisms6040117 - 26 Nov 2018
Cited by 23 | Viewed by 4652
Abstract
Salmonella can cause enteric diseases in humans and a wide range of animals, and even outbreaks of foodborne illness. The aim of this study was to investigate the frequency and distribution of serovars, and antimicrobial resistance in Salmonella isolates from pigs with diarrhea [...] Read more.
Salmonella can cause enteric diseases in humans and a wide range of animals, and even outbreaks of foodborne illness. The aim of this study was to investigate the frequency and distribution of serovars, and antimicrobial resistance in Salmonella isolates from pigs with diarrhea in 26 provinces in China from 2014 to 2016. A total of 104 Salmonella isolates were identified and the dominant serovar was S. 4,[5],12:i:- (53.9%). All Salmonella isolates were resistant to trimethoprim-sulfamethoxazole, and many were resistant to ampicillin (80.8%) and tetracycline (76.9%). Among 104 Salmonella isolates, aac(6′)-Ib-cr was the dominant plasmid-mediated quinolone resistance gene (80.8%), followed by qnrS (47.1%). The pulsed-field gel electrophoresis results suggest that the Salmonella isolates from different regions were genetically diverse, and ST34 was the most prevalent. S. 4,[5],12:i:- isolates is the widespread presence of heavy metal tolerance genes. The fact that the same sequence types were found in different regions and the high similarity coefficient of S. 4,[5],12:i:- isolates from different regions indicate the clonal expansion of the isolates, and the isolates carried various antimicrobial resistance genes. The multidrug resistant Salmonella can be widely detected in pigs, which will present a challenge for farm husbandry. Full article
(This article belongs to the Special Issue Biocontrol of Food Borne Pathogens)
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13 pages, 1344 KiB  
Article
Inclusion Body Bead Size in E. coli Controlled by Physiological Feeding
by Julian Kopp, Christoph Slouka, Daniel Strohmer, Julian Kager, Oliver Spadiut and Christoph Herwig
Microorganisms 2018, 6(4), 116; https://doi.org/10.3390/microorganisms6040116 - 25 Nov 2018
Cited by 19 | Viewed by 6065
Abstract
The Gram-negative bacterium E. coli is the host of choice for producing a multitude of recombinant proteins relevant in the pharmaceutical industry. Generally, cultivation is easy, media are cheap, and a high product titer can be obtained. However, harsh induction procedures combined with [...] Read more.
The Gram-negative bacterium E. coli is the host of choice for producing a multitude of recombinant proteins relevant in the pharmaceutical industry. Generally, cultivation is easy, media are cheap, and a high product titer can be obtained. However, harsh induction procedures combined with the usage of IPTG (isopropyl β-d-1 thiogalactopyranoside) as an inducer are often believed to cause stress reactions, leading to intracellular protein aggregates, which are so known as so-called inclusion bodies (IBs). Downstream applications in bacterial processes cause the bottleneck in overall process performance, as bacteria lack many post-translational modifications, resulting in time and cost-intensive approaches. Especially purification of inclusion bodies is notoriously known for its long processing times and low yields. In this contribution, we present screening strategies for determination of inclusion body bead size in an E. coli-based bioprocess producing exclusively inclusion bodies. Size can be seen as a critical quality attribute (CQA), as changes in inclusion body behavior have a major effect on subsequent downstream processing. A model-based approach was used, aiming to trigger a distinct inclusion body size: Physiological feeding control, using qs,C as a critical process parameter, has a high impact on inclusion body size and could be modelled using a hyperbolic saturation mechanism calculated in form of a cumulated substrate uptake rate. Within this model, the sugar uptake rate of the cells, in the form of the cumulated sugar uptake-value, was simulated and considered being a key performance indicator for determination of the desired size. We want to highlight that the usage of the mentioned screening strategy in combination with a model-based approach will allow tuning of the process towards a certain inclusion body size using a qs based control only. Optimized inclusion body size at the time-point of harvest should stabilize downstream processing and, therefore, increase the overall time-space yield. Furthermore, production of distinct inclusion body size may be interesting for application as a biocatalyst and nanoparticulate material. Full article
(This article belongs to the Special Issue Recombinant Protein Expression in Microorganisms)
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34 pages, 2700 KiB  
Review
Modulation of Enterohaemorrhagic Escherichia coli Survival and Virulence in the Human Gastrointestinal Tract
by Grégory Jubelin, Mickaël Desvaux, Stephanie Schüller, Lucie Etienne-Mesmin, Maite Muniesa and Stéphanie Blanquet-Diot
Microorganisms 2018, 6(4), 115; https://doi.org/10.3390/microorganisms6040115 - 19 Nov 2018
Cited by 42 | Viewed by 9299
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) is a major foodborne pathogen responsible for human diseases ranging from diarrhoea to life-threatening complications. Survival of the pathogen and modulation of virulence gene expression along the human gastrointestinal tract (GIT) are key features in bacterial pathogenesis, but remain [...] Read more.
Enterohaemorrhagic Escherichia coli (EHEC) is a major foodborne pathogen responsible for human diseases ranging from diarrhoea to life-threatening complications. Survival of the pathogen and modulation of virulence gene expression along the human gastrointestinal tract (GIT) are key features in bacterial pathogenesis, but remain poorly described, due to a paucity of relevant model systems. This review will provide an overview of the in vitro and in vivo studies investigating the effect of abiotic (e.g., gastric acid, bile, low oxygen concentration or fluid shear) and biotic (e.g., gut microbiota, short chain fatty acids or host hormones) parameters of the human gut on EHEC survival and/or virulence (especially in relation with motility, adhesion and toxin production). Despite their relevance, these studies display important limitations considering the complexity of the human digestive environment. These include the evaluation of only one single digestive parameter at a time, lack of dynamic flux and compartmentalization, and the absence of a complex human gut microbiota. In a last part of the review, we will discuss how dynamic multi-compartmental in vitro models of the human gut represent a novel platform for elucidating spatial and temporal modulation of EHEC survival and virulence along the GIT, and provide new insights into EHEC pathogenesis. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
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12 pages, 3890 KiB  
Article
Role of SCFAs for Fimbrillin-Dependent Biofilm Formation of Actinomyces oris
by Itaru Suzuki, Takehiko Shimizu and Hidenobu Senpuku
Microorganisms 2018, 6(4), 114; https://doi.org/10.3390/microorganisms6040114 - 13 Nov 2018
Cited by 12 | Viewed by 3887
Abstract
Actinomyces oris expresses type 1 and 2 fimbriae on the cell surface. Type 2 fimbriae mediate co-aggregation and biofilm formation and are composed of the shaft fimbrillin FimA and the tip fimbrillin FimB. Short-chain fatty acids (SCFAs) are metabolic products of oral bacteria, [...] Read more.
Actinomyces oris expresses type 1 and 2 fimbriae on the cell surface. Type 2 fimbriae mediate co-aggregation and biofilm formation and are composed of the shaft fimbrillin FimA and the tip fimbrillin FimB. Short-chain fatty acids (SCFAs) are metabolic products of oral bacteria, but the effects of exogenous SCFAs on FimA-dependent biofilm formation are poorly understood. We performed two types of biofilm formation assays using A. oris MG1 or MG1.ΔfimA to observe the effects of SCFAs on FimA-dependent biofilm formation in 96-well and six-well microtiter plates and a flow cell system. SCFAs did not induce six- and 16-hour biofilm formation of A. oris MG1 and MG1.ΔfimA in saliva-coated 96-well and six-well microtiter plates in which metabolites produced during growth were not excluded. However, 6.25 mM butyric acid and 3.125 mM propionic acid induced FimA-dependent biofilm formation and cell death in a flow cell system in which metabolites produced during growth were excluded. Metabolites produced during growth may lead to disturbing effects of SCFAs on the biofilm formation. The pure effects of SCFAs on biofilm formation were induction of FimA-dependent biofilm formation, but the stress responses from dead cells may regulate its effects. Therefore, SCFA may play a key role in A. oris biofilm formation. Full article
(This article belongs to the Special Issue Oral Microbiota in Health and Disease)
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16 pages, 4699 KiB  
Article
Enzymes Catalyzing the TCA- and Urea Cycle Influence the Matrix Composition of Biofilms Formed by Methicillin-Resistant Staphylococcus aureus USA300
by Sarah De Backer, Julia Sabirova, Ines De Pauw, Henri De Greve, Jean-Pierre Hernalsteens, Herman Goossens and Surbhi Malhotra-Kumar
Microorganisms 2018, 6(4), 113; https://doi.org/10.3390/microorganisms6040113 - 29 Oct 2018
Cited by 26 | Viewed by 5504
Abstract
In methicillin-sensitive Staphylococcus aureus (MSSA), the tricarboxylic acid (TCA) cycle is known to negatively regulate production of the major biofilm-matrix exopolysaccharide, PIA/PNAG. However, methicillin-resistant S. aureus (MRSA) produce a primarily proteinaceous biofilm matrix, and contribution of the TCA-cycle therein remains unclear. Utilizing USA300-JE2 [...] Read more.
In methicillin-sensitive Staphylococcus aureus (MSSA), the tricarboxylic acid (TCA) cycle is known to negatively regulate production of the major biofilm-matrix exopolysaccharide, PIA/PNAG. However, methicillin-resistant S. aureus (MRSA) produce a primarily proteinaceous biofilm matrix, and contribution of the TCA-cycle therein remains unclear. Utilizing USA300-JE2 Tn-mutants (NARSA) in genes encoding TCA- and urea cycle enzymes for transduction into a prolific biofilm-forming USA300 strain (UAS391-Erys), we studied the contribution of the TCA- and urea cycle and of proteins, eDNA and PIA/PNAG, to the matrix. Genes targeted in the urea cycle encoded argininosuccinate lyase and arginase (argH::Tn and rocF::Tn), and in the TCA-cycle encoded succinyl-CoA synthetase, succinate dehydrogenase, aconitase, isocitrate dehydrogenase, fumarate hydratase class II, and citrate synthase II (sucC::Tn, sdhA/B::Tn, acnA::Tn, icd::Tn, fumC::Tn and gltA::Tn). Biofilm formation was significantly decreased under no flow and flow conditions by argH::Tn, fumC::Tn, and sdhA/B::Tn (range OD492 0.374−0.667; integrated densities 2.065−4.875) compared to UAS391-EryS (OD492 0.814; integrated density 10.676) (p ≤ 0.008). Cellular and matrix stains, enzymatic treatment (Proteinase K, DNase I), and reverse-transcriptase PCR-based gene-expression analysis of fibronectin-binding proteins (fnbA/B) and the staphylococcal accessory regulator (sarA) on pre-formed UAS391-Erys and Tn-mutant biofilms showed: (i) < 1% PIA/PNAG in the proteinaceous/eDNA matrix; (ii) increased proteins under no flow and flow in the matrix of Tn mutant biofilms (on average 50 and 51 (±11)%) compared to UAS391-Erys (on average 22 and 25 (±4)%) (p < 0.001); and (iii) down- and up-regulation of fnbA/B and sarA, respectively, in Tn-mutants compared to UAS391-EryS (0.62-, 0.57-, and 2.23-fold on average). In conclusion, we show that the biofilm matrix of MRSA-USA300 and the corresponding Tn mutants is PIA/PNAG-independent and are mainly composed of proteins and eDNA. The primary impact of TCA-cycle inactivation was on the protein component of the biofilm matrix of MRSA-USA300. Full article
(This article belongs to the Special Issue Staphylococcus aureus Infection and Antimicrobial Resistance)
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8 pages, 1607 KiB  
Article
Novel Effector Protein EspY3 of Type III Secretion System from Enterohemorrhagic Escherichia coli Is Localized in Actin Pedestals
by Mariano Larzábal, Wanderson Marques Da Silva, Nahuel A. Riviere and Ángel A. Cataldi
Microorganisms 2018, 6(4), 112; https://doi.org/10.3390/microorganisms6040112 - 27 Oct 2018
Cited by 10 | Viewed by 4241
Abstract
Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic Escherichia coli (EPEC) are attaching and effacing (A/E) pathogens, which translocate effector proteins to intestinal enterocytes through a type III secretion system (T3SS). T3SS and most of its effector proteins are encoded in a pathogenicity island called [...] Read more.
Enterohemorrhagic Escherichia coli (EHEC) and enteropathogenic Escherichia coli (EPEC) are attaching and effacing (A/E) pathogens, which translocate effector proteins to intestinal enterocytes through a type III secretion system (T3SS). T3SS and most of its effector proteins are encoded in a pathogenicity island called LEE. Recently, new effectors have been located outside the LEE. This study aimed to characterize EspY3, a novel non-LEE encoded T3SS effector of EHEC. EspY3 shares homology with SopD and PipB2 effector proteins of Salmonella’s T3SS-1 and T3SS-2, respectively. The presence of recombinant EspY3 in the supernatant samples demonstrated that EspY3 was secreted by the T3SS of EHEC and EPEC. Through infection assays, we demonstrated the translocation of EspY3 into Caco-2 cells by T3SS of EPEC. The subcellular localization of EspY3 was determined in the pedestal region, where its presence generates a significant increase in the size of the pedestals area. The EspY3 effector induced the elongation of polymerized actin pedestals in infected Caco-2 by EPEC. This study confirmed that EspY3 is part of the repertoire of T3SS effectors of EHEC O157:H7, and that it participates in modeling cellular actin during the infection. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
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10 pages, 511 KiB  
Review
Shiga Toxin-Producing Escherichia coli Infections during Pregnancy
by Flavia Sacerdoti, María Luján Scalise, Juliana Burdet, María Marta Amaral, Ana María Franchi and Cristina Ibarra
Microorganisms 2018, 6(4), 111; https://doi.org/10.3390/microorganisms6040111 - 23 Oct 2018
Cited by 12 | Viewed by 7819
Abstract
Gastrointestinal infection with Shiga toxin-producing Escherichia coli (STEC) causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS), characterized by hemolytic anemia, thrombocytopenia and acute renal failure. The main virulence factor of STEC is Shiga toxin (Stx), which is responsible for HUS development. STEC [...] Read more.
Gastrointestinal infection with Shiga toxin-producing Escherichia coli (STEC) causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome (HUS), characterized by hemolytic anemia, thrombocytopenia and acute renal failure. The main virulence factor of STEC is Shiga toxin (Stx), which is responsible for HUS development. STEC can produce Stx type 1 and/or 2 (Stx1, Stx2) and their variants, Stx2 being more frequently associated with severe cases of HUS. This pathology occurs in 5–15% of cases with STEC infection when Stx gain access to the bloodstream and causes damage in the target organs such as the kidney and brain. STEC infections affect mainly young children, although the large HUS outbreak with a new Stx2-producing STEC O104:H4 in Europe in 2011 involved more adults than children, and women were over-represented. Maternal infections during pregnancy are associated with adverse pregnancy outcomes. Studies in rats showed that Stx2 binds to the utero-placental unit and causes adverse pregnancy outcomes. In this article, we provide a brief overview of Stx2 action on placental tissues and discuss whether they might cause pregnancy loss or preterm birth. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
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46 pages, 1965 KiB  
Review
Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA
by Hiroyuki Hori, Takuya Kawamura, Takako Awai, Anna Ochi, Ryota Yamagami, Chie Tomikawa and Akira Hirata
Microorganisms 2018, 6(4), 110; https://doi.org/10.3390/microorganisms6040110 - 20 Oct 2018
Cited by 36 | Viewed by 7828
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered [...] Read more.
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science. Full article
(This article belongs to the Special Issue Thermophiles and Thermozymes)
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10 pages, 889 KiB  
Article
Molecular Tunnels in Enzymes and Thermophily: A Case Study on the Relationship to Growth Temperature
by Juan Miguel Gonzalez
Microorganisms 2018, 6(4), 109; https://doi.org/10.3390/microorganisms6040109 - 20 Oct 2018
Cited by 3 | Viewed by 3713
Abstract
Developments in protein expression, analysis and computational capabilities are decisively contributing to a better understanding of the structure of proteins and their relationship to function. Proteins are known to be adapted to the growth rate of microorganisms and some microorganisms (named (hyper)thermophiles) thrive [...] Read more.
Developments in protein expression, analysis and computational capabilities are decisively contributing to a better understanding of the structure of proteins and their relationship to function. Proteins are known to be adapted to the growth rate of microorganisms and some microorganisms (named (hyper)thermophiles) thrive optimally at high temperatures, even above 100 °C. Nevertheless, some biomolecules show great instability at high temperatures and some of them are universal and required substrates and cofactors in multiple enzymatic reactions for all (both mesophiles and thermophiles) living cells. Only a few possibilities have been pointed out to explain the mechanisms that thermophiles use to successfully thrive under high temperatures. As one of these alternatives, the role of molecular tunnels or channels in enzymes has been suggested but remains to be elucidated. This study presents an analysis of channels in proteins (i.e., substrate tunnels), comparing two different protein types, glutamate dehydrogenase and glutamine phosphoribosylpyrophosphate amidotransferase, which are supposed to present a different strategy on the requirement for substrate tunnels with low and high needs for tunneling, respectively. The search and comparison of molecular tunnels in these proteins from microorganisms thriving optimally from 15 °C to 100 °C suggested that those tunnels in (hyper)thermophiles are required and optimized to specific dimensions at high temperatures for the enzyme glutamine phosphoribosylpyrophosphate amidotransferase. For the enzyme glutamate dehydrogenase, a reduction of empty spaces within the protein could explain the optimization at increasing temperatures. This analysis provides further evidence on molecular channeling as a feasible mechanism in hyperthermophiles with multiple relevant consequences contributing to better understand how they live under those extreme conditions. Full article
(This article belongs to the Special Issue Thermophiles and Thermozymes)
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13 pages, 1356 KiB  
Article
Contribution of the Oligomeric State to the Thermostability of Isoenzyme 3 from Candida rugosa
by María-Efigenia Álvarez-Cao, Roberto González, María A. Pernas and María Luisa Rúa
Microorganisms 2018, 6(4), 108; https://doi.org/10.3390/microorganisms6040108 - 19 Oct 2018
Cited by 17 | Viewed by 3380
Abstract
Thermophilic proteins have evolved different strategies to maintain structure and function at high temperatures; they have large, hydrophobic cores, and feature increased electrostatic interactions, with disulfide bonds, salt-bridging, and surface charges. Oligomerization is also recognized as a mechanism for protein stabilization to confer [...] Read more.
Thermophilic proteins have evolved different strategies to maintain structure and function at high temperatures; they have large, hydrophobic cores, and feature increased electrostatic interactions, with disulfide bonds, salt-bridging, and surface charges. Oligomerization is also recognized as a mechanism for protein stabilization to confer a thermophilic adaptation. Mesophilic proteins are less thermostable than their thermophilic homologs, but oligomerization plays an important role in biological processes on a wide variety of mesophilic enzymes, including thermostabilization. The mesophilic yeast Candida rugosa contains a complex family of highly related lipase isoenzymes. Lip3 has been purified and characterized in two oligomeric states, monomer (mLip3) and dimer (dLip3), and crystallized in a dimeric conformation, providing a perfect model for studying the effects of homodimerization on mesophilic enzymes. We studied kinetics and stability at different pHs and temperatures, using the response surface methodology to compare both forms. At the kinetic level, homodimerization expanded Lip3 specificity (serving as a better catalyst on soluble substrates). Indeed, dimerization increased its thermostability by more than 15 °C (maximum temperature for dLip3 was out of the experimental range; >50 °C), and increased the pH stability by nearly one pH unit, demonstrating that oligomerization is a viable strategy for the stabilization of mesophilic enzymes. Full article
(This article belongs to the Special Issue Thermophiles and Thermozymes)
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13 pages, 229 KiB  
Review
Leaky Gut, Leaky Brain?
by Mark E. M. Obrenovich
Microorganisms 2018, 6(4), 107; https://doi.org/10.3390/microorganisms6040107 - 18 Oct 2018
Cited by 189 | Viewed by 35370
Abstract
‘Leaky gut’ syndrome, long-associated with celiac disease, has attracted much attention in recent years and for decades, was widely known in complementary/alternative medicine circles. It is often described as an increase in the permeability of the intestinal mucosa, which could allow bacteria, toxic [...] Read more.
‘Leaky gut’ syndrome, long-associated with celiac disease, has attracted much attention in recent years and for decades, was widely known in complementary/alternative medicine circles. It is often described as an increase in the permeability of the intestinal mucosa, which could allow bacteria, toxic digestive metabolites, bacterial toxins, and small molecules to ‘leak’ into the bloodstream. Nervous system involvement with celiac disease is know to occur even at subclinical levels. Gluten and gluten sensitivity are considered to trigger this syndrome in individuals genetically predisposed to celiac disease. However, the incidence of celiac disease in the general population is quite low. Nevertheless, increased public interest in gluten sensitivity has contributed to expanded food labels stating ‘gluten-free’ and the proliferation of gluten-free products, which further drives gluten-free lifestyle changes by individuals without frank celiac disease. Moreover, systemic inflammation is associated with celiac disease, depression, and psychiatric comorbidities. This mini-review focuses on the possible neurophysiological basis of leaky gut; leaky brain disease; and the microbiota’s contribution to inflammation, gastrointestinal, and blood-brain barrier integrity, in order to build a case for possible mechanisms that could foster further ‘leaky’ syndromes. We ask whether a gluten-free diet is important for anyone or only those with celiac disease. Full article
(This article belongs to the Special Issue Gut Microbiota Diversity Relates to Lifestyle)
15 pages, 3279 KiB  
Article
Rational Design and Biotechnological Production of Novel AfpB-PAF26 Chimeric Antifungal Proteins
by Marcos Heredero, Sandra Garrigues, Mónica Gandía, Jose F. Marcos and Paloma Manzanares
Microorganisms 2018, 6(4), 106; https://doi.org/10.3390/microorganisms6040106 - 15 Oct 2018
Cited by 7 | Viewed by 5004
Abstract
Antimicrobial peptides (AMPs) have been proposed as candidates to develop new antimicrobial compounds for medicine, agriculture, and food preservation. PAF26 is a synthetic antifungal hexapeptide obtained from combinatorial approaches with potent fungicidal activity against filamentous fungi. Other interesting AMPs are the antifungal proteins [...] Read more.
Antimicrobial peptides (AMPs) have been proposed as candidates to develop new antimicrobial compounds for medicine, agriculture, and food preservation. PAF26 is a synthetic antifungal hexapeptide obtained from combinatorial approaches with potent fungicidal activity against filamentous fungi. Other interesting AMPs are the antifungal proteins (AFPs) of fungal origin, which are basic cysteine-rich and small proteins that can be biotechnologically produced in high amounts. A promising AFP is the AfpB identified in the phytopathogen Penicillium digitatum. In this work, we aimed to rationally design, biotechnologically produce and test AfpB::PAF26 chimeric proteins to obtain designed AFPs (dAfpBs) with improved properties. The dAfpB6 and dAfpB9 chimeras could be produced using P. digitatum as biofactory and a previously described Penicillium chrysogenum-based expression cassette, but only dAfpB9 could be purified and characterized. Protein dAfpB9 showed subtle and fungus-dependent differences of fungistatic activity against filamentous fungi compared to native AfpB. Significantly, dAfpB9 lost the fungicidal activity of PAF26 and AfpB, thus disconnecting this activity from the fungistatic activity and mapping fungicidal determinants to the exposed loop L3 of AfpB, wherein modifications are located. This study provides information on the design and development of novel chimeric AFPs. Full article
(This article belongs to the Special Issue Antimicrobial Proteins in Filamentous Fungi)
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13 pages, 1420 KiB  
Article
Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds
by Luka Šafarič, Sepehr Shakeri Yekta, Tong Liu, Bo H. Svensson, Anna Schnürer, David Bastviken and Annika Björn
Microorganisms 2018, 6(4), 105; https://doi.org/10.3390/microorganisms6040105 - 11 Oct 2018
Cited by 13 | Viewed by 4320
Abstract
Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a [...] Read more.
Knowledge of microbial community dynamics in relation to process perturbations is fundamental to understand and deal with the instability of anaerobic digestion (AD) processes. This study aims to investigate the microbial community structure and function of a thermophilic AD process, fed with a chemically defined substrate, and its association with process performance stability. Next generation amplicon sequencing of 16S ribosomal RNA (rRNA) genes revealed that variations in relative abundances of the predominant bacterial species, Defluviitoga tunisiensis and Anaerobaculum hydrogeniformans, were not linked to the process performance stability, while dynamics of bacterial genera of low abundance, Coprothermobacter and Defluviitoga (other than D. tunisiensis), were associated with microbial community function and process stability. A decrease in the diversity of the archaeal community was observed in conjunction with process recovery and stable performance, implying that the high abundance of specific archaeal group(s) contributed to the stable AD. Dominance of hydrogenotrophic Methanoculleus particularly corresponded to an enhanced microbial acetate and propionate turnover capacity, whereas the prevalence of hydrogenotrophic Methanothermobacter and acetoclastic Methanosaeta was associated with instable AD. Acetate oxidation via syntrophic interactions between Coprothermobacter and Methanoculleus was potentially the main methane-formation pathway during the stable process. We observed that supplementation of Se and W to the medium improved the propionate turnover by the thermophilic consortium. The outcomes of our study provided insights into the community dynamics and trace element requirements in relation to the process performance stability of thermophilic AD. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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15 pages, 260 KiB  
Review
Role of Natural Volatiles and Essential Oils in Extending Shelf Life and Controlling Postharvest Microorganisms of Small Fruits
by Toktam Taghavi, Chyer Kim and Alireza Rahemi
Microorganisms 2018, 6(4), 104; https://doi.org/10.3390/microorganisms6040104 - 5 Oct 2018
Cited by 40 | Viewed by 5880
Abstract
Small fruits are a multi-billion dollar industry in the US, and are economically important in many other countries. However, they are perishable and susceptible to physiological disorders and biological damage. Food safety and fruit quality are the major concerns of the food chain [...] Read more.
Small fruits are a multi-billion dollar industry in the US, and are economically important in many other countries. However, they are perishable and susceptible to physiological disorders and biological damage. Food safety and fruit quality are the major concerns of the food chain from farm to consumer, especially with increasing regulations in recent years. At present, the industry depends on pesticides and fungicides to control food spoilage organisms. However, due to consumer concerns and increasing demand for safer produce, efforts are being made to identify eco-friendly compounds that can extend the shelf life of small fruits. Most volatiles and essential oils produced by plants are safe for humans and the environment, and lots of research has been conducted to test the in vitro efficacy of single-compound volatiles or multi-compound essential oils on various microorganisms. However, there are not many reports on their in vivo (in storage) and In situ (in the field) applications. In this review, we discuss the efficacy, minimum inhibitory concentrations, and mechanisms of action of volatiles and essential oils that control microorganisms (bacteria and fungi) on small fruits such as strawberries, raspberries, blueberries, blackberries, and grapes under the three conditions. Full article
(This article belongs to the Special Issue Advances in Prevention of Foodborne Pathogens of Public Health Concern during Manufacturing)
18 pages, 1884 KiB  
Article
Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities
by Susanne Günther, Daniela Becker, Thomas Hübschmann, Susann Reinert, Sabine Kleinsteuber, Susann Müller and Christian Wilhelm
Microorganisms 2018, 6(4), 103; https://doi.org/10.3390/microorganisms6040103 - 4 Oct 2018
Cited by 13 | Viewed by 4756
Abstract
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived [...] Read more.
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived from engineered algae. The microbial community structure was measured on the single cell level using flow cytometry. Abiotic and operational reactor parameters were analyzed in parallel. The R-based tool flowCyBar facilitated visualization of community dynamics and indicated sub-communities involved in glycolate fermentation and methanogenesis. Cell sorting and amplicon sequencing of 16S rRNA and mcrA genes were used to identify the key organisms involved in the anaerobic conversion process. The microbial community allowed a constant fermentation, although it was sensitive to high glycolate concentrations in the feed. A linear correlation between glycolate loading rate and biogas amount was observed (R2 = 0.99) for glycolate loading rates up to 1.81 g L−1 day−1 with a maximum in biogas amount of 3635 mL day−1 encompassing 45% methane. The cytometric diversity remained high during the whole cultivation period. The dominating bacterial genera were Syntrophobotulus, Clostridia genus B55_F, Aminobacterium, and Petrimonas. Methanogenesis was almost exclusively performed by the hydrogenotrophic genus Methanobacterium. Full article
(This article belongs to the Special Issue Metabolic Diversity of Anaerobic Microbial Communities)
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12 pages, 3331 KiB  
Article
Synergism of Mild Heat and High-Pressure Pasteurization Against Listeria monocytogenes and Natural Microflora in Phosphate-Buffered Saline and Raw Milk
by Abimbola Allison, Shahid Chowdhury and Aliyar Fouladkhah
Microorganisms 2018, 6(4), 102; https://doi.org/10.3390/microorganisms6040102 - 3 Oct 2018
Cited by 15 | Viewed by 3875
Abstract
As many as 99% of illnesses caused by Listeria monocytogenes are foodborne in nature, leading to 94% hospitalizations, and are responsible for the collective annual deaths of 266 American adults. The current study is a summary of microbiological hurdle validation studies to investigate [...] Read more.
As many as 99% of illnesses caused by Listeria monocytogenes are foodborne in nature, leading to 94% hospitalizations, and are responsible for the collective annual deaths of 266 American adults. The current study is a summary of microbiological hurdle validation studies to investigate synergism of mild heat (up to 55 °C) and elevated hydrostatic pressure (up to 380 MPa) for decontamination of Listeria monocytogenes and natural background microflora in raw milk and phosphate-buffered saline. At 380 MPa, for treatments of 0 to 12 min, d-values of 3.47, 3.15, and 2.94 were observed for inactivation of the pathogen at 4, 25, and 50 °C. Up to 3.73 and >4.26 log CFU/mL reductions (p < 0.05) of habituated Listeria monocytogenes were achieved using pressure at 380 MPa for 3 and 12 min, respectively. Similarly, background microflora counts were reduced (p < 0.05) by 1.3 and >2.4 log CFU/mL after treatments at 380 MPa for 3 and 12 min, respectively. Treatments below three min were less efficacious (p ≥ 0.05) against the pathogen and background microflora, in the vast majority of time and pressure combinations. Results of this study could be incorporated as part of a risk-based food safety management system and risk assessment analyses for mitigating the public health burden of listeriosis. Full article
(This article belongs to the Special Issue Advances in Prevention of Foodborne Pathogens of Public Health Concern during Manufacturing)
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15 pages, 1439 KiB  
Article
A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice
by Yuri Yamamoto, Yumiko Nakanishi, Shinnosuke Murakami, Wanping Aw, Tomoya Tsukimi, Ryoko Nozu, Masami Ueno, Kyoji Hioki, Kenji Nakahigashi, Akiyoshi Hirayama, Masahiro Sugimoto, Tomoyoshi Soga, Mamoru Ito, Masaru Tomita and Shinji Fukuda
Microorganisms 2018, 6(4), 101; https://doi.org/10.3390/microorganisms6040101 - 29 Sep 2018
Cited by 23 | Viewed by 5701
Abstract
Commensal microbiota colonize the surface of our bodies. The inside of the gastrointestinal tract is one such surface that provides a habitat for them. The gastrointestinal tract is a long organ system comprising of various parts, and each part possesses various functions. It [...] Read more.
Commensal microbiota colonize the surface of our bodies. The inside of the gastrointestinal tract is one such surface that provides a habitat for them. The gastrointestinal tract is a long organ system comprising of various parts, and each part possesses various functions. It has been reported that the composition of intestinal luminal metabolites between the small and large intestine are different; however, comprehensive metabolomic and commensal microbiota profiles specific to each part of the gastrointestinal lumen remain obscure. In this study, by using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS)-based metabolome and 16S rRNA gene-based microbiome analyses of specific pathogen-free (SPF) and germ-free (GF) murine gastrointestinal luminal profiles, we observed the different roles of commensal microbiota in each part of the gastrointestinal tract involved in carbohydrate metabolism and nutrient production. We found that the concentrations of most amino acids in the SPF small intestine were higher than those in the GF small intestine. Furthermore, sugar alcohols such as mannitol and sorbitol accumulated only in the GF large intestine, but not in the SPF large intestine. On the other hand, pentoses, such as arabinose and xylose, gradually accumulated from the cecum to the colon only in SPF mice, but were undetected in GF mice. Correlation network analysis between the gastrointestinal microbes and metabolites showed that niacin metabolism might be correlated to Methylobacteriaceae. Collectively, commensal microbiota partially affects the gastrointestinal luminal metabolite composition based on their metabolic dynamics, in cooperation with host digestion and absorption. Full article
(This article belongs to the Special Issue Gastrointestinal Microbiota Impacts Human Health and Disease)
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8 pages, 243 KiB  
Brief Report
Antimicrobial Resistance in Class 1 Integron-Positive Shiga Toxin-Producing Escherichia coli Isolated from Cattle, Pigs, Food and Farm Environment
by Rocío Colello, Alejandra Krüger, José Di Conza, John W. A. Rossen, Alexander W. Friedrich, Gabriel Gutkind, Analía I. Etcheverría and Nora L. Padola
Microorganisms 2018, 6(4), 99; https://doi.org/10.3390/microorganisms6040099 - 28 Sep 2018
Cited by 14 | Viewed by 4330
Abstract
The aim of this study was to investigate the presence of class 1 integrons in a collection of Shiga toxin-producing Escherichia coli (STEC) from different origins and to characterize pheno- and genotypically the antimicrobial resistance associated to them. A collection of 649 isolates [...] Read more.
The aim of this study was to investigate the presence of class 1 integrons in a collection of Shiga toxin-producing Escherichia coli (STEC) from different origins and to characterize pheno- and genotypically the antimicrobial resistance associated to them. A collection of 649 isolates were screened for the class 1 integrase gene (intI1) by Polymerase chain reaction The variable region of class 1 integrons was amplified and sequenced. Positive strains were evaluated for the presence of antimicrobial resistance genes with microarray and for antimicrobial susceptibility by the disk diffusion method. Seven out of 649 STEC strains some to serogroups, O26, O103 and O130 isolated from cattle, chicken burger, farm environment and pigs were identified as positive for intl1. Different arrangements of gene cassettes were detected in the variable region of class 1 integron: dfrA16, aadA23 and dfrA1-aadA1. In almost all strains, phenotypic resistance to streptomycin, tetracycline, trimethoprim/sulfamethoxazole, and sulfisoxazole was observed. Microarray analyses showed that most of the isolates carried four or more antimicrobial resistance markers and STEC strains were categorized as Multridrug-resistant. Although antimicrobials are not usually used in the treatment of STEC infections, the presence of Multridrug-resistant in isolates collected from farm and food represents a risk for animal and human health. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
19 pages, 759 KiB  
Review
Recent Advances in Shiga Toxin-Producing Escherichia coli Research in Latin America
by Alfredo G. Torres, Maria M. Amaral, Leticia Bentancor, Lucia Galli, Jorge Goldstein, Alejandra Krüger and Maricarmen Rojas-Lopez
Microorganisms 2018, 6(4), 100; https://doi.org/10.3390/microorganisms6040100 - 28 Sep 2018
Cited by 44 | Viewed by 7385
Abstract
Pathogenic Escherichia coli are known to be a common cause of diarrheal disease and a frequently occurring bacterial infection in children and adults in Latin America. Despite the effort to combat diarrheal infections, the south of the American continent remains a hot spot [...] Read more.
Pathogenic Escherichia coli are known to be a common cause of diarrheal disease and a frequently occurring bacterial infection in children and adults in Latin America. Despite the effort to combat diarrheal infections, the south of the American continent remains a hot spot for infections and sequelae associated with the acquisition of one category of pathogenic E. coli, the Shiga toxin-producing E. coli (STEC). This review will focus on an overview of the prevalence of different STEC serotypes in human, animals and food products, focusing on recent reports from Latin America outlining the recent research progress achieved in this region to combat disease and endemicity in affected countries and to improve understanding on emerging serotypes and their virulence factors. Furthermore, this review will highlight the progress done in vaccine development and treatment and will also discuss the effort of the Latin American investigators to respond to the thread of STEC infections by establishing a multidisciplinary network of experts that are addressing STEC-associated animal, human and environmental health issues, while trying to reduce human disease. Regardless of the significant scientific contributions to understand and combat STEC infections worldwide, many significant challenges still exist and this review has focus in the Latin American efforts as an example of what can be accomplished when multiple groups have a common goal. Full article
(This article belongs to the Special Issue Pathogenesis of Enterohaemorrhagic Escherichia coli)
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