Microorganisms

11 pages, 1860 KiB

Open AccessCase Report

Ceftolozane-Tazobactam Treatment of Hypervirulent Multidrug Resistant Pseudomonas aeruginosa Infections in Neutropenic Patients

by Paolo E. Coppola, Paolo Gaibani, Chiara Sartor, Simone Ambretti, Russell E. Lewis, Claudia Sassi, Marco Pignatti, Stefania Paolini, Antonio Curti, Fausto Castagnetti, Margherita Ursi, Michele Cavo and Marta Stanzani

Microorganisms 2020, 8(12), 2055; https://doi.org/10.3390/microorganisms8122055 - 21 Dec 2020

Cited by 4 | Viewed by 3622

Abstract

The effectiveness of ceftolozane/tazobactam for the treatment of infections in neutropenic patients caused by hypervirulent multidrug-resistant (MDR) Pseudomonas aeruginosa has not been previously reported. We identified seven cases of MDR P. aeruginosa infection in neutropenic patients over a four-month period within the same [...] Read more.

The effectiveness of ceftolozane/tazobactam for the treatment of infections in neutropenic patients caused by hypervirulent multidrug-resistant (MDR) Pseudomonas aeruginosa has not been previously reported. We identified seven cases of MDR P. aeruginosa infection in neutropenic patients over a four-month period within the same hematology ward. Four cases were associated with rapid progression despite piperacillin-tazobactam or meropenem therapy, and three patients developed sepsis or extensive skin/soft tissue necrosis. In three of the four cases, patients were empirically switched from meropenem to ceftolozane/avibactam before carbapenem susceptibility test results were available, and all four patients underwent extensive surgical debridement or amputation of affected tissues and survived. Further investigation revealed a common bathroom source of MDR P. aeruginosa clonal subtypes ST175 and ST235 that harbored genes for type III secretion system expression and elaboration of ExoU or ExoS exotoxin. We conclude that ceftolozane/tazobactam plus early source control was critical for control of rapidly progressing skin and soft infection in these neutropenic patients caused by highly virulent ST175 and ST235 clones of MDR P. aeruginosa. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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14 pages, 1392 KiB

Open AccessArticle

Presence of Infection by Mycobacterium avium subsp. paratuberculosis in the Blood of Patients with Crohn’s Disease and Control Subjects Shown by Multiple Laboratory Culture and Antibody Methods

by J. Todd Kuenstner, Raghava Potula, Tim J. Bull, Irene R. Grant, Antonio Foddai, Saleh A. Naser, Horacio Bach, Peilin Zhang, Daohai Yu, Xiaoning Lu and Ira Shafran

Microorganisms 2020, 8(12), 2054; https://doi.org/10.3390/microorganisms8122054 - 21 Dec 2020

Cited by 18 | Viewed by 5965

Abstract

Mycobacterium avium subspecies paratuberculosis (MAP) has long been suspected to be involved in the etiology of Crohn’s disease (CD). An obligate intracellular pathogen, MAP persists and influences host macrophages. The primary goals of this study were to test new rapid culture methods for [...] Read more.

Mycobacterium avium subspecies paratuberculosis (MAP) has long been suspected to be involved in the etiology of Crohn’s disease (CD). An obligate intracellular pathogen, MAP persists and influences host macrophages. The primary goals of this study were to test new rapid culture methods for MAP in human subjects and to assess the degree of viable culturable MAP bacteremia in CD patients compared to controls. A secondary goal was to compare the efficacy of three culture methods plus a phage assay and four antibody assays performed in separate laboratories, to detect MAP from the parallel samples. Culture and serological MAP testing was performed blind on whole blood samples obtained from 201 subjects including 61 CD patients (two of the patients with CD had concurrent ulcerative colitis (UC)) and 140 non-CD controls (14 patients in this group had UC only). Viable MAP bacteremia was detected in a significant number of study subjects across all groups. This included Pozzato culture (124/201 or 62% of all subjects, 35/61 or 57% of CD patients), Phage assay (113/201 or 56% of all subjects, 28/61 or 46% of CD patients), TiKa culture (64/201 or 32% of all subjects, 22/61 or 36% of CD patients) and MGIT culture (36/201 or 18% of all subjects, 15/61 or 25% of CD patients). A link between MAP detection and CD was observed with MGIT culture and one of the antibody methods (Hsp65) confirming previous studies. Other detection methods showed no association between any of the groups tested. Nine subjects with a positive Phage assay (4/9) or MAP culture (5/9) were again positive with the Phage assay one year later. This study highlights viable MAP bacteremia is widespread in the study population including CD patients, those with other autoimmune conditions and asymptomatic healthy subjects. Full article

(This article belongs to the Section Medical Microbiology)

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6 pages, 837 KiB

Open AccessCommunication

Thermal Inactivation of Different Capripox Virus Isolates

by Janika Wolff, Martin Beer and Bernd Hoffmann

Microorganisms 2020, 8(12), 2053; https://doi.org/10.3390/microorganisms8122053 - 21 Dec 2020

Cited by 4 | Viewed by 2850

Abstract

Capripox viruses (CaPVs) cause a highly contagious poxvirus disease of livestock animals. Working with CaPVs requires laboratories with a high biosecurity level (BSL 3), and reliable inactivation of these viruses is therefore necessary for working in areas or laboratories with a lower biosecurity [...] Read more.

Capripox viruses (CaPVs) cause a highly contagious poxvirus disease of livestock animals. Working with CaPVs requires laboratories with a high biosecurity level (BSL 3), and reliable inactivation of these viruses is therefore necessary for working in areas or laboratories with a lower biosecurity status. Heat treatment provides a simple and well-established tool for the inactivation due to its substantial advantages (e.g., easy to perform, fast, cheap, and robust). In our study, we determined the time–temperature profiles needed for a fail-safe inactivation procedure using four different CaPV isolates in aqueous solution with and without the addition of protective serum. All four tested CaPV isolates were completely inactivated after 30 min at 56 °C or 10 min at 60 °C. Since different thermal stabilities of other CaPV isolates could not be fully excluded, we recommend an inactivation procedure of 1 h at 56 °C for safe shipment or working in laboratories with lower biosecurity levels than BSL 3. Full article

(This article belongs to the Special Issue Capripoxviruses: A Continuing Worldwide Threat to Sheep, Goats and Cattle)

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7 pages, 245 KiB

Open AccessCommunication

Molecular Characterization of Staphylococcus aureus Isolated from Chronic Infected Wounds in Rural Ghana

by Manuel Wolters, Hagen Frickmann, Martin Christner, Anna Both, Holger Rohde, Kwabena Oppong, Charity Wiafe Akenten, Jürgen May and Denise Dekker

Microorganisms 2020, 8(12), 2052; https://doi.org/10.3390/microorganisms8122052 - 21 Dec 2020

Cited by 11 | Viewed by 3295

Abstract

Background: Globally, Staphylococcus aureus is an important bacterial pathogen causing a wide range of community and hospital acquired infections. In Ghana, resistance of S. aureus to locally available antibiotics is increasing but the molecular basis of resistance and the population structure of S. [...] Read more.

Background: Globally, Staphylococcus aureus is an important bacterial pathogen causing a wide range of community and hospital acquired infections. In Ghana, resistance of S. aureus to locally available antibiotics is increasing but the molecular basis of resistance and the population structure of S. aureus in particular in chronic wounds are poorly described. However, this information is essential to understand the underlying mechanisms of resistance and spread of resistant clones. We therefore subjected 28 S. aureus isolates from chronic infected wounds in a rural area of Ghana to whole genome sequencing. Results: Overall, resistance of S. aureus to locally available antibiotics was high and 29% were Methicillin resistant Staphylococcus aureus (MRSA). The most abundant sequence type was ST88 (29%, 8/28) followed by ST152 (18%, 5/28). All ST88 carried the mecA gene, which was associated with this sequence type only. Chloramphenicol resistance gene fexB was exclusively associated with the methicillin-resistant ST88 strains. Panton-Valentine leukocidin (PVL) carriage was associated with ST121 and ST152. Other detected mechanisms of resistance included dfrG, conferring resistance to trimethoprim. Conclusions: This study provides valuable information for understanding the population structure and resistance mechanisms of S. aureus isolated from chronic wound infections in rural Ghana. Full article

(This article belongs to the Special Issue Staphylococcal Infections (Host and Pathogenic Factors))

14 pages, 11135 KiB

Open AccessArticle

Integrative and Conjugative Element ICETh1 Functions as a Pangenomic DNA Capture Module in Thermus thermophilus

by Alba Blesa, Ignacio Baquedano, Sandra González-de la Fuente, Mario Mencía and José Berenguer

Microorganisms 2020, 8(12), 2051; https://doi.org/10.3390/microorganisms8122051 - 21 Dec 2020

Cited by 2 | Viewed by 2461

Abstract

Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within [...] Read more.

Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within an integrative and conjugative element (ICETh1) in the strain Tth HB27, whereas the NCA is constitutively expressed in both mates. Previous experiments suggested the presence of multiple origins of transfer along the genome, which could generate genomic mosaicity among the progeny. Here, we designed transjugation experiments between two closely related strains of Tth with highly syntenic genomes, containing enough single nucleotide polymorphisms to allow precise parenthood analysis. Individual clones from the progeny were sequenced, revealing their origin as derivatives of our ICETh1-containing intended “donor” strain (HB27), which had acquired separate fragments from the genome of the ICETh1-free HB8 cells, which are our intended recipient. Due to the bidirectional nature of transjugation, only assays employing competence-defective HB27 derivatives as donors allowed the recovery of HB8-derived progeny. These results show a preference for a retrotransfer mechanism in transjugation in ICETh1-bearing strains, supporting an inter-strain gene-capture function for ICETh1. This function could benefit the donor-capable host by facilitating the acquisition of adaptive traits from external sources, ultimately increasing the open pangenome of Thermus, maximizing the potential repertoire of physiological and phenotypical traits related to adaptation and speciation. Full article

(This article belongs to the Special Issue Bacterial Genomes and Evolution by Horizontal Gene Transfer (HGT))

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Graphical abstract

18 pages, 1432 KiB

Open AccessReview

The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale

by Daniel Craig Zielinski, Arjun Patel and Bernhard O. Palsson

Microorganisms 2020, 8(12), 2050; https://doi.org/10.3390/microorganisms8122050 - 21 Dec 2020

Cited by 10 | Viewed by 4781

Abstract

Microbial strains are being engineered for an increasingly diverse array of applications, from chemical production to human health. While traditional engineering disciplines are driven by predictive design tools, these tools have been difficult to build for biological design due to the complexity of [...] Read more.

Microbial strains are being engineered for an increasingly diverse array of applications, from chemical production to human health. While traditional engineering disciplines are driven by predictive design tools, these tools have been difficult to build for biological design due to the complexity of biological systems and many unknowns of their quantitative behavior. However, due to many recent advances, the gap between design in biology and other engineering fields is closing. In this work, we discuss promising areas of development of computational tools for engineering microbial strains. We define five frontiers of active research: (1) Constraint-based modeling and metabolic network reconstruction, (2) Kinetics and thermodynamic modeling, (3) Protein structure analysis, (4) Genome sequence analysis, and (5) Regulatory network analysis. Experimental and machine learning drivers have enabled these methods to improve by leaps and bounds in both scope and accuracy. Modern strain design projects will require these tools to be comprehensively applied to the entire cell and efficiently integrated within a single workflow. We expect that these frontiers, enabled by the ongoing revolution of big data science, will drive forward more advanced and powerful strain engineering strategies. Full article

(This article belongs to the Special Issue Genome-Scale Modeling of Microorganisms in the Real World)

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19 pages, 2423 KiB

Open AccessArticle

Genotyping Study of Salmonella 4,[5],12:i:- Monophasic Variant of Serovar Typhimurium and Characterization of the Second-Phase Flagellar Deletion by Whole Genome Sequencing

by Ainhoa Arrieta-Gisasola, Aitor Atxaerandio-Landa, Victoria Garrido, María Jesús Grilló, Ilargi Martínez-Ballesteros, Lorena Laorden, Javier Garaizar and Joseba Bikandi

Microorganisms 2020, 8(12), 2049; https://doi.org/10.3390/microorganisms8122049 - 21 Dec 2020

Cited by 13 | Viewed by 3248

Abstract

After Salmonella Enteritidis and S. Typhimurium, S. 4,[5],12:i:- is the most reported serovar in human clinical cases. During the past 20 years, many tools have been used for its typing and second-phase flagellar deletion characterization. Currently, whole genome sequencing (WGS) and different bioinformatic [...] Read more.

After Salmonella Enteritidis and S. Typhimurium, S. 4,[5],12:i:- is the most reported serovar in human clinical cases. During the past 20 years, many tools have been used for its typing and second-phase flagellar deletion characterization. Currently, whole genome sequencing (WGS) and different bioinformatic programs have shown the potential to be more accurate than earlier tools. To assess this potential, we analyzed by WGS and in silico typing a selection of 42 isolates of S. 4,[5],12:i:- and S. Typhimurium with different in vitro characteristics. Comparative analysis showed that SeqSero2 does not differentiate fljB-positive S. 4,[5],12:i:- strains from those of serovar Typhimurium. Our results proved that the strains selected for this work were non-clonal S. 4,[5],12:i:- strains circulating in Spain. Using WGS data, we identified 13 different deletion types of the second-phase flagellar genomic region. Most of the deletions were generated by IS26 insertions, showing orientation-dependent conserved deletion ends. In addition, we detected S. 4,[5],12:i:- strains of the American clonal line that would give rise to the Southern European clone in Spain. Our results suggest that new S. 4,[5],12:i:- strains are continuously emerging from different S. Typhimurium strains via different genetic events, at least in swine products. Full article

(This article belongs to the Special Issue Salmonella and Salmonellosis)

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14 pages, 754 KiB

Open AccessReview

Role of Respiratory Syncytial Virus in Pediatric Pneumonia

by Sonia Bianchini, Ettore Silvestri, Alberto Argentiero, Valentina Fainardi, Giovanna Pisi and Susanna Esposito

Microorganisms 2020, 8(12), 2048; https://doi.org/10.3390/microorganisms8122048 - 21 Dec 2020

Cited by 34 | Viewed by 12445

Abstract

Respiratory viral infections represent the leading cause of hospitalization in infants and young children worldwide and the second leading cause of infant mortality. Among these, Respiratory Syncytial Virus (RSV) represents the main cause of lower respiratory tract infections (LRTIs) in young children worldwide. [...] Read more.

Respiratory viral infections represent the leading cause of hospitalization in infants and young children worldwide and the second leading cause of infant mortality. Among these, Respiratory Syncytial Virus (RSV) represents the main cause of lower respiratory tract infections (LRTIs) in young children worldwide. RSV manifestation can range widely from mild upper respiratory infections to severe respiratory infections, mainly bronchiolitis and pneumonia, leading to hospitalization, serious complications (such as respiratory failure), and relevant sequalae in childhood and adulthood (wheezing, asthma, and hyperreactive airways). There are no specific clinical signs or symptoms that can distinguish RSV infection from other respiratory pathogens. New multiplex platforms offer the possibility to simultaneously identify different pathogens, including RSV, with an accuracy similar to that of single polymerase chain reaction (PCR) in the majority of cases. At present, the treatment of RSV infection relies on supportive therapy, mainly consisting of oxygen and hydration. Palivizumab is the only prophylactic method available for RSV infection. Advances in technology and scientific knowledge have led to the creation of different kinds of vaccines and drugs to treat RSV infection. Despite the good level of these studies, there are currently few registered strategies to prevent or treat RSV due to difficulties related to the unpredictable nature of the disease and to the specific target population. Full article

(This article belongs to the Special Issue Respiratory Tract Infection in Children)

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13 pages, 3170 KiB

Open AccessArticle

Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs

by Svetlana E. Belova, Olga V. Danilova, Anastasia A. Ivanova, Alexander Y. Merkel and Svetlana N. Dedysh

Microorganisms 2020, 8(12), 2047; https://doi.org/10.3390/microorganisms8122047 - 21 Dec 2020

Cited by 10 | Viewed by 3253

Abstract

Upland soils of tundra function as a constant sink for atmospheric CH₄ but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH₄-C m⁻² day⁻¹ were determined by [...] Read more.

Upland soils of tundra function as a constant sink for atmospheric CH₄ but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH₄-C m⁻² day⁻¹ were determined by the static chamber method in a mildly acidic upland soil of the lichen-dominated forested tundra, North Siberia, Russia. The maximal CH₄ oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the pmoA gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these pmoA gene fragments by means of specific qPCR assay detected ~10⁷pmoA gene copies g⁻¹ dry soil. The pmoA diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to pmoA of Candidatus Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order Methylococcales and the family Methylocystaceae. The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated Beijerinckiaceae bacteria. These reads displayed 96–100 and 95–98% sequence similarity to 16S rRNA gene of Candidatus Methyloaffinis lahnbergensis and “Methylocapsa gorgona” MG08, respectively, and were represented by eight species-level operational taxonomic units (OTUs), two of which were highly abundant. These identification results characterize subarctic upland soils, which are exposed to atmospheric methane concentrations only, as a unique habitat colonized mostly by USCα methanotrophs. Full article

(This article belongs to the Special Issue Biology, Diversity, and Ecology of Methanotrophic Bacteria)

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1 pages, 152 KiB

Open AccessCorrection

Correction: Yoo, J.Y., et al. Gut Microbiota and Immune System Interactions. Microorganisms 2020, 8, 1587

by Ji Youn Yoo, Maureen Groer, Samia Valeria Ozorio Dutra, Anujit Sarkar and Daniel Ian McSkimming

Microorganisms 2020, 8(12), 2046; https://doi.org/10.3390/microorganisms8122046 - 21 Dec 2020

Cited by 20 | Viewed by 2709

Abstract

Corrections have been made to “Gut Microbiota and Immune System Interactions” [...] Full article

7 pages, 457 KiB

Open AccessCommunication

Hepatitis E Virus in Manure and Its Removal by Psychrophilic anaerobic Biodigestion in Intensive Production Farms, Santa Catarina, Brazil, 2018–2019

by Doris Sobral Marques Souza, Deisi Cristine Tápparo, Paula Rogovski, Rafael Dorighello Cadamuro, Estêvão Brasiliense de Souza, Raphael da Silva, Roberto Degenhardt, Juliano De Dea Lindner, Aline Viancelli, William Michelon, Airton Kunz, Helen Treichel, Marta Hernández, David Rodríguez-Lázaro and Gislaine Fongaro

Microorganisms 2020, 8(12), 2045; https://doi.org/10.3390/microorganisms8122045 - 21 Dec 2020

Cited by 7 | Viewed by 3348

Abstract

Hepatitis E virus (HEV) is an important enteric agent that can circulate in swine; it is excreted in manure, and of zoonotic interest. The present study investigated, by RT-qPCR, the circulation of HEV in swine manure from different types of pig farms (maternity, [...] Read more.

Hepatitis E virus (HEV) is an important enteric agent that can circulate in swine; it is excreted in manure, and of zoonotic interest. The present study investigated, by RT-qPCR, the circulation of HEV in swine manure from different types of pig farms (maternity, nursery, and grow-finish farms) in Santa Catarina State, the major pig production area of Brazil, and also evaluated the HEV removal efficiency of psychrophilic anaerobic biodigesters (PABs). While HEV was consistently detected in manure from grow-finish pig farms (>4 log HEV genome copies (GC) L⁻¹), the virus was not detected in manure from maternity and nursery farms. These findings suggest a potential high biosafety status during primary-swine production, with a subsequent contamination in grow-finish production. The anaerobic biodigestion process reduced more than 2 log₁₀ HEV GC in the processed swine manure. However, the virus concentration in final effluent remained high, with an average value of 3.85 log₁₀ HEV GC L⁻¹. Consequently, our results demonstrate that PABs can be a robust tool for effective inactivation of HEV, while reinforcing the need for sanitary surveillance and legislation of swine manure-derived biofertilizers, to avoid the spread of zoonotic enteric pathogens such as HEV. Full article

(This article belongs to the Special Issue Hepatitis E Virus, an Emergent Foodborne Pathogen? Public Health Implications)

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7 pages, 1560 KiB

Open AccessCommunication

Time-Resolved Observation of the Destination of Microinjected Potato Spindle Tuber Viroid (PSTVd) in the Abaxial Leaf Epidermal Cells of Nicotiana benthamiana

by Hyesu Seo, Ying Wang and Woong June Park

Microorganisms 2020, 8(12), 2044; https://doi.org/10.3390/microorganisms8122044 - 20 Dec 2020

Cited by 6 | Viewed by 2837

Abstract

Viroids are single-stranded noncoding RNA molecules of 250–400 nucleotides that cause plant diseases. One of the two families of viroids is Pospiviroidae, the members of which replicate in the nuclei of host cells. To replicate in plants, viroids of Pospiviroidae must enter the [...] Read more.

Viroids are single-stranded noncoding RNA molecules of 250–400 nucleotides that cause plant diseases. One of the two families of viroids is Pospiviroidae, the members of which replicate in the nuclei of host cells. To replicate in plants, viroids of Pospiviroidae must enter the nucleus. However, the nuclear import of viroids remains understudied. In this work, we documented the time-dependent characteristics of the changes in microinjected fluorescently labeled potato spindle tuber viroid (PSTVd). The cytoplasmic fluorescence disappeared gradually, with only nuclear fluorescence remaining as the PSTVd injected in the cytoplasm was imported into the nucleus. Through this work, we determined that the time for half-maximal nuclear accumulation of the viroid was about 23 min. Interestingly, we found some cells where the nuclear import did not occur, despite the high level of cytosolic viroid injected. In some cells, the injected viroids disappeared within 10–20 min. The nuclear import of PSTVd is not a simple concentration-dependent process but was probably under the regulation of diverse factors that may be missing from some cells used for our observation. Full article

(This article belongs to the Special Issue Viroids)

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26 pages, 1895 KiB

Open AccessArticle

Identification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning

by Shawn M. Higdon, Bihua C. Huang, Alan B. Bennett and Bart C. Weimer

Microorganisms 2020, 8(12), 2043; https://doi.org/10.3390/microorganisms8122043 - 20 Dec 2020

Cited by 19 | Viewed by 4687

Abstract

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized [...] Read more.

Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an ‘unknown’ annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism. Full article

(This article belongs to the Section Plant Microbe Interactions)

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15 pages, 2186 KiB

Open AccessArticle

Rumen and Hindgut Bacteria Are Potential Indicators for Mastitis of Mid-Lactating Holstein Dairy Cows

by Yifan Zhong, Ming-Yuan Xue, Hui-Zeng Sun, Teresa G. Valencak, Le Luo Guan and Jianxin Liu

Microorganisms 2020, 8(12), 2042; https://doi.org/10.3390/microorganisms8122042 - 20 Dec 2020

Cited by 17 | Viewed by 3812

Abstract

Mastitis is one of the major problems for the productivity of dairy cows and its classifications have usually been based on milk somatic cell counts (SCCs). In this study, we investigated the differences in milk production, rumen fermentation parameters, and diversity and composition [...] Read more.

Mastitis is one of the major problems for the productivity of dairy cows and its classifications have usually been based on milk somatic cell counts (SCCs). In this study, we investigated the differences in milk production, rumen fermentation parameters, and diversity and composition of rumen and hindgut bacteria in cows with similar SCCs with the aim to identify whether they can be potential microbial biomarkers to improve the diagnostics of mastitis. A total of 20 dairy cows with SCCs over 500 × 10³ cells/mL in milk but without clinical symptoms of mastitis were selected in this study. Random forest modeling revealed that Erysipelotrichaceae UCG 004 and the [Eubacterium] xylanophilum group in the rumen, as well as the Family XIII AD3011 group and Bacteroides in the hindgut, were the most influential candidates as key bacterial markers for differentiating “true” mastitis from cows with high SCCs. Mastitis statuses of 334 dairy cows were evaluated, and 96 in 101 cows with high SCCs were defined as healthy rather than mastitis according to the rumen bacteria. Our findings suggested that bacteria in the rumen and hindgut can be a new approach and provide an opportunity to reduce common errors in the detection of mastitis. Full article

(This article belongs to the Special Issue Gut Microbiome and Aging)

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2 pages, 151 KiB

Open AccessEditorial

Editorial for the Special Issue: Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections

by Hirokazu Kimura, Yuriko Hayashi, Mitsuru Sada, Haruyuki Ishii, Takeshi Tsugawa and Akihide Ryo

Microorganisms 2020, 8(12), 2041; https://doi.org/10.3390/microorganisms8122041 - 20 Dec 2020

Viewed by 1945

Abstract

In Japan, there is a proverb that the common cold is associated with all diseases [...] Full article

(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections)

14 pages, 3176 KiB

Open AccessArticle

Comparative Gut Microbiome Differences between Ferric Citrate and Calcium Carbonate Phosphate Binders in Patients with End-Stage Kidney Disease

by Ping-Hsun Wu, Po-Yu Liu, Yi-Wen Chiu, Wei-Chun Hung, Yi-Ting Lin, Ting-Yun Lin, Szu-Chun Hung, Rachel Ann Delicano, Mei-Chuan Kuo and Chun-Ying Wu

Microorganisms 2020, 8(12), 2040; https://doi.org/10.3390/microorganisms8122040 - 20 Dec 2020

Cited by 16 | Viewed by 5151

Abstract

Gut dysbiosis in patients with chronic kidney disease (CKD) may induce chronic inflammation and increase morbidity. Phosphate-binding agents, generally used in patients with CKD, may potentially change the composition of the gut microbiota. This study aimed to compare the microbiota composition in hemodialysis [...] Read more.

Gut dysbiosis in patients with chronic kidney disease (CKD) may induce chronic inflammation and increase morbidity. Phosphate-binding agents, generally used in patients with CKD, may potentially change the composition of the gut microbiota. This study aimed to compare the microbiota composition in hemodialysis patients treated with ferric citrate or calcium carbonate. The stool microbiota was investigated in hemodialysis patients treated with ferric citrate (n = 8) and calcium carbonate (n = 46) using 16S rRNA gene amplicon sequencing profiling using linear discriminant analysis of effect size. Further predictive functional profiling of microbial communities was obtained with Tax4Fun in R. Hemodialysis patients treated with calcium carbonate had a significantly reduced microbial species diversity (Shannon index and Simpson index) and an increased microbial alteration ratio compared with patients treated with ferric citrate. A distinct microbial community structure was found in patients treated with ferric citrate, with an increased abundance of the Bacteroidetes phylum and a decreased abundance of the phylum Firmicutes. Members of the order Lactobacillales were enriched in patients treated with calcium carbonate, whereas taxa of the genera Ruminococcaceae UCG-004, Flavonifractor, and Cronobacter were enriched in patients treated with ferric citrate phosphate binder. In conclusion, Ferric citrate therapy results in a more diverse microbiome community compared to calcium carbonate therapy in hemodialysis patients with phosphate binder treatment. The gut microbiome reflects the phosphate binder choice in hemodialysis patients, further affecting the physiological environment in the gastrointestinal tract. Full article

(This article belongs to the Special Issue Gastrointestinal Microbiota and Gut Barrier Impact Human Health and Disease)

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15 pages, 3170 KiB

Open AccessArticle

H89 Treatment Reduces Intestinal Inflammation and Candida albicans Overgrowth in Mice

by Corentin Dumortier, Rogatien Charlet, Ali Bettaieb and Samir Jawhara

Microorganisms 2020, 8(12), 2039; https://doi.org/10.3390/microorganisms8122039 - 19 Dec 2020

Cited by 6 | Viewed by 3070

Abstract

Deregulation of the dynamic crosstalk between the gut microbiota, intestinal epithelial cells, and immune cells is critically involved in the development of inflammatory bowel disease and the overgrowth of opportunistic pathogens, including the human opportunistic fungus Candida albicans. In the present study, [...] Read more.

Deregulation of the dynamic crosstalk between the gut microbiota, intestinal epithelial cells, and immune cells is critically involved in the development of inflammatory bowel disease and the overgrowth of opportunistic pathogens, including the human opportunistic fungus Candida albicans. In the present study, we assessed the effect of N-[2-(p-bromocinnamylamino)ethyl]-5-isoquinolinesulfonamide (H89), a protein kinase A inhibitor, on the migration of macrophages to C. albicans through dextran sulphate sodium (DSS)-challenged Caco-2 cells. We also investigated the impact of H89 on intestinal inflammation and C. albicans clearance from the gut, and determined the diversity of the gut microbiota in a murine model of DSS-induced colitis. H89 reduced the migration of macrophages to C. albicans through DSS-challenged Caco-2 cells. In addition, H89 decreased C. albicans viability and diminished the expression of pro-inflammatory cytokines and innate immune receptors in macrophages and colonic epithelial Caco-2 cells. In mice with DSS-induced colitis, H89 attenuated the clinical and histological scores of inflammation and promoted the elimination of C. albicans from the gut. H89 administration to mice decreased the overgrowth of Escherichia coli and Enterococcus faecalis populations while Lactobacillus johnsonii populations increased significantly. Overall, H89 reduced intestinal inflammation and promoted the elimination of C. albicans from the gut. Full article

(This article belongs to the Special Issue Human Pathogenic Fungi: Host-Pathogen Interactions and Virulence)

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12 pages, 2061 KiB

Open AccessArticle

Differential Response of Mycorrhizal Plants to Tomato bushy stunt virus and Tomato mosaic virus Infection

by Neda Khoshkhatti, Omid Eini, Davoud Koolivand, Antreas Pogiatzis, John N. Klironomos and Sepideh Pakpour

Microorganisms 2020, 8(12), 2038; https://doi.org/10.3390/microorganisms8122038 - 19 Dec 2020

Cited by 9 | Viewed by 3059

Abstract

Tomato bushy stunt virus (TBSV) and Tomato mosaic virus (ToMV) are important economic pathogens in tomato fields. Rhizoglomus irregulare is a species of arbuscular mycorrhizal (AM) fungus that provides nutrients to host plants. To understand the effect of R. irregulare on the infection [...] Read more.

Tomato bushy stunt virus (TBSV) and Tomato mosaic virus (ToMV) are important economic pathogens in tomato fields. Rhizoglomus irregulare is a species of arbuscular mycorrhizal (AM) fungus that provides nutrients to host plants. To understand the effect of R. irregulare on the infection by TBSV/ToMV in tomato plants, in a completely randomized design, five treatments, including uninfected control plants without AM fungi (C), uninfected control plants with AM fungi (M) TBSV/ToMV-infected plants without AM fungi (V), TBSV/ToMV-infected plants before mycorrhiza (VM) inoculation, and inoculated plants with mycorrhiza before TBSV/ToMV infection (MV), were studied. Factors including viral RNA accumulation and expression of Pathogenesis Related proteins (PR) coding genes including PR1, PR2, and PR3 in the young leaves were measured. For TBSV, a lower level of virus accumulation and a higher expression of PR genes in MV plants were observed compared to V and VM plants. In contrast, for ToMV, a higher level of virus accumulation and a lower expression of PR genes in MV plants were observed as compared to V and VM plants. These results indicated that mycorrhizal symbiosis reduces or increases the viral accumulation possibly via the regulation of PR genes in tomato plants. Full article

(This article belongs to the Special Issue Mycorrhizal Fungi)

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23 pages, 3060 KiB

Open AccessReview

Aspergillosis, Avian Species and the One Health Perspective: The Possible Importance of Birds in Azole Resistance

by Aryse Martins Melo, David A. Stevens, Lisa A. Tell, Cristina Veríssimo, Raquel Sabino and Melissa Orzechowski Xavier

Microorganisms 2020, 8(12), 2037; https://doi.org/10.3390/microorganisms8122037 - 19 Dec 2020

Cited by 33 | Viewed by 7855

Abstract

The One Health context considers health based on three pillars: humans, animals, and environment. This approach is a strong ally in the surveillance of infectious diseases and in the development of prevention strategies. Aspergillus spp. are fungi that fit substantially in this context, [...] Read more.

The One Health context considers health based on three pillars: humans, animals, and environment. This approach is a strong ally in the surveillance of infectious diseases and in the development of prevention strategies. Aspergillus spp. are fungi that fit substantially in this context, in view of their ubiquity, as well as their importance as plant pathogens, and potentially fatal pathogens for, particularly, humans and avian species. In addition, the emergence of azole resistance, mainly in Aspergillus fumigatus sensu stricto, and the proven role of fungicides widely used on crops, reinforces the need for a multidisciplinary approach to this problem. Avian species are involved in short and long distance travel between different types of landscapes, such as agricultural fields, natural environments and urban environments. Thus, birds can play an important role in the dispersion of Aspergillus, and of special concern, azole-resistant strains. In addition, some bird species are particularly susceptible to aspergillosis. Therefore, avian aspergillosis could be considered as an environmental health indicator. In this review, aspergillosis in humans and birds will be discussed, with focus on the presence of Aspergillus in the environment. We will relate these issues with the emergence of azole resistance on Aspergillus. These topics will be therefore considered and reviewed from the “One Health” perspective. Full article

(This article belongs to the Special Issue Aspergillus and Health 1.0)

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12 pages, 1458 KiB

Open AccessCommunication

SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data

by Tristan Cardon, Isabelle Fournier and Michel Salzet

Microorganisms 2020, 8(12), 2036; https://doi.org/10.3390/microorganisms8122036 - 19 Dec 2020

Cited by 3 | Viewed by 3027

Abstract

Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics have led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the [...] Read more.

Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics have led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the reference ORF or from ncRNAs. These alternative proteins (AltProts) are not represented in the conventional protein databases and this “ghost proteome” was not considered until recently. Some of these proteins are functional and there is growing evidence that they are involved in central functions in physiological and physiopathological context. Based on our experience with AltProts, we were interested in finding out their interaction with the viral protein coming from the SARS-CoV-2 virus, responsible for the 2020 COVID-19 outbreak. Thus, we have scrutinized the recently published data by Krogan and coworkers (2020) on the SARS-CoV-2 interactome with host cells by affinity purification in co-immunoprecipitation (co-IP) in the perspective of drug repurposing. The initial work revealed the interaction between 332 human cellular reference proteins (RefProts) with the 27 viral proteins. Re-interrogation of this data using 23 viral targets and including AltProts, followed by enrichment of the interaction networks, leads to identify 218 RefProts (in common to initial study), plus 56 AltProts involved in 93 interactions. This demonstrates the necessity to take into account the ghost proteome for discovering new therapeutic targets, and establish new therapeutic strategies. Missing the ghost proteome in the drug metabolism and pharmacokinetic (DMPK) drug development pipeline will certainly be a major limitation to the establishment of efficient therapies. Full article

(This article belongs to the Special Issue SARS-CoV-2: Epidemiology and Pathogenesis)

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11 pages, 269 KiB

Open AccessArticle

Does Antimicrobial Therapy Affect Mortality of Patients with Carbapenem-Resistant Klebsiella pneumoniae Bacteriuria? A Nationwide Multicenter Study in Taiwan

by Chien Chuang, Chin-Fang Su, Jung-Chung Lin, Po-Liang Lu, Ching-Tai Huang, Jann-Tay Wang, Yin-Ching Chuang, L. Kristopher Siu, Chang-Phone Fung and Yi-Tsung Lin

Microorganisms 2020, 8(12), 2035; https://doi.org/10.3390/microorganisms8122035 - 19 Dec 2020

Cited by 4 | Viewed by 2153

Abstract

Few clinical studies have previously discussed patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) bacteriuria. This study aimed to assess the effect of antimicrobial therapy on the mortality of patients with CRKP bacteriuria. Hospitalized adults with CRKP bacteriuria were enrolled retrospectively from 16 hospitals in [...] Read more.

Few clinical studies have previously discussed patients with carbapenem-resistant Klebsiella pneumoniae (CRKP) bacteriuria. This study aimed to assess the effect of antimicrobial therapy on the mortality of patients with CRKP bacteriuria. Hospitalized adults with CRKP bacteriuria were enrolled retrospectively from 16 hospitals in Taiwan during 2013 and 2014. Critically ill patients were defined as those with an Acute Physiology and Chronic Health Evaluation (APACHE) II score ≥ 20. Multivariate Cox regression analysis was used to determine independent risk factors for 14- and 28-day mortality. Of 107 patients with CRKP bacteriuria, the 14-day and 28-day mortality was 14.0% and 25.2%, respectively. Thirty-three patients received appropriate antimicrobial therapy. In the multivariate Cox regression analysis, the APACHE II score ≥ 20 was the only independent risk factor for 14-day mortality (hazard ratio [HR]: 6.15, p = 0.024). APACHE II score ≥ 20 (HR: 3.05, p = 0.018) and male sex (HR: 2.57, p = 0.037) were associated with 28-day mortality. Among critically ill patients with CRKP bacteriuria, appropriate antimicrobial therapy was not associated with 14-day or 28-day survival. In conclusion, in patients with CRKP bacteriuria, the use of appropriate antimicrobial therapy was not an independent factor associated with reduced mortality. Our findings may inform future antibiotic stewardship interventions for bacteriuria caused by multidrug resistant pathogens. Full article

(This article belongs to the Special Issue Carbapenemase-producing Enterobacteriaceae)

17 pages, 2281 KiB

Open AccessArticle

Targeted Genome Mining—From Compound Discovery to Biosynthetic Pathway Elucidation

by Nils Gummerlich, Yuriy Rebets, Constanze Paulus, Josef Zapp and Andriy Luzhetskyy

Microorganisms 2020, 8(12), 2034; https://doi.org/10.3390/microorganisms8122034 - 19 Dec 2020

Cited by 6 | Viewed by 3311

Abstract

Natural products are an important source of novel investigational compounds in drug discovery. Especially in the field of antibiotics, Actinobacteria have been proven to be a reliable source for lead structures. The discovery of these natural products with activity- and structure-guided screenings has [...] Read more.

Natural products are an important source of novel investigational compounds in drug discovery. Especially in the field of antibiotics, Actinobacteria have been proven to be a reliable source for lead structures. The discovery of these natural products with activity- and structure-guided screenings has been impeded by the constant rediscovery of previously identified compounds. Additionally, a large discrepancy between produced natural products and biosynthetic potential in Actinobacteria, including representatives of the order Pseudonocardiales, has been revealed using genome sequencing. To turn this genomic potential into novel natural products, we used an approach including the in-silico pre-selection of unique biosynthetic gene clusters followed by their systematic heterologous expression. As a proof of concept, fifteen Saccharothrixespanaensis genomic library clones covering predicted biosynthetic gene clusters were chosen for expression in two heterologous hosts, Streptomyceslividans and Streptomycesalbus. As a result, two novel natural products, an unusual angucyclinone pentangumycin and a new type II polyketide synthase shunt product SEK90, were identified. After purification and structure elucidation, the biosynthetic pathways leading to the formation of pentangumycin and SEK90 were deduced using mutational analysis of the biosynthetic gene cluster and feeding experiments with ¹³C-labelled precursors. Full article

(This article belongs to the Section Microbial Biotechnology)

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16 pages, 1652 KiB

Open AccessArticle

Effects of Ectomycorrhizal Fungi and Heavy Metals (Pb, Zn, and Cd) on Growth and Mineral Nutrition of Pinus halepensis Seedlings in North Africa

by Chadlia Hachani, Mohammed S. Lamhamedi, Claudio Cameselle, Susana Gouveia, Abdenbi Zine El Abidine, Damase P. Khasa and Zoubeir Béjaoui

Microorganisms 2020, 8(12), 2033; https://doi.org/10.3390/microorganisms8122033 - 19 Dec 2020

Cited by 33 | Viewed by 4524

Abstract

The pollution of soils by heavy metals resulting from mining activities is one of the major environmental problems in North Africa. Mycorrhizoremediation using mycorrhizal fungi and adapted plant species is emerging as one of the most innovative methods to remediate heavy metal pollution. [...] Read more.

The pollution of soils by heavy metals resulting from mining activities is one of the major environmental problems in North Africa. Mycorrhizoremediation using mycorrhizal fungi and adapted plant species is emerging as one of the most innovative methods to remediate heavy metal pollution. This study aims to assess the growth and the nutritional status of ectomycorrhizal Pinus halepensis seedlings subjected to high concentrations of Pb, Zn, and Cd for possible integration in the restoration of heavy metals contaminated sites. Ectomycorrhizal and non-ectomycorrhizal P. halepensis seedlings were grown in uncontaminated (control) and contaminated soils for 12 months. Growth, mineral nutrition, and heavy metal content were assessed. Results showed that ectomycorrhizae significantly improved shoot and roots dry masses of P. halepensis seedlings, as well as nitrogen shoot content. The absorption of Pb, Zn, and Cd was much higher in the roots than in the shoots, and significantly more pronounced in ectomycorrhizal seedlings—especially for Zn and Cd. The presence of ectomycorrhizae significantly reduced the translocation factor of Zn and Cd and bioaccumulation factor of Pb and Cd, which enhanced the phytostabilizing potential of P. halepensis seedlings. These results support the use of ectomycorrhizal P. halepensis in the remediation of heavy metal contaminated sites. Full article

(This article belongs to the Special Issue Mycorrhizal Fungi)

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20 pages, 2417 KiB

Open AccessArticle

Assessing the Multivariate Relationship between the Human Infant Intestinal Exfoliated Cell Transcriptome (Exfoliome) and Microbiome in Response to Diet

by Kejun He, Sharon M. Donovan, Ivan V. Ivanov, Jennifer S. Goldsby, Laurie A. Davidson and Robert S. Chapkin

Microorganisms 2020, 8(12), 2032; https://doi.org/10.3390/microorganisms8122032 - 18 Dec 2020

Cited by 8 | Viewed by 4097

Abstract

Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly influencing the health and well-being of the host. In addition to the standard differential expression analysis of host genes to assess the complex cross-talk between [...] Read more.

Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly influencing the health and well-being of the host. In addition to the standard differential expression analysis of host genes to assess the complex cross-talk between environment (diet), microbiome, and host intestinal physiology, data-driven integrative approaches are needed to identify potential biomarkers of both host genes and microbial communities that characterize these interactions. Our findings demonstrate that the complementary application of univariate differential gene expression analysis and multivariate approaches such as sparse Canonical Correlation Analysis (sCCA) and sparse Principal Components Analysis (sPCA) can be used to integrate data from both the healthy infant gut microbial community and host transcriptome (exfoliome) using stool derived exfoliated cells shed from the gut. These approaches reveal host genes and microbial functional categories related to the feeding phenotype of the infants. Our findings also confirm that combinatorial noninvasive -omic approaches provide an integrative genomics-based perspective of neonatal host-gut microbiome interactions. Full article

(This article belongs to the Special Issue Novel Insights into the Infant Gut Microbiome and Host–Microbe Interactions)

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12 pages, 479 KiB

Open AccessArticle

Genes on the Move: In Vitro Transduction of Antimicrobial Resistance Genes between Human and Canine Staphylococcal Pathogens

by Sian Marie Frosini, Ross Bond, Alex J. McCarthy, Claudia Feudi, Stefan Schwarz, Jodi A. Lindsay and Anette Loeffler

Microorganisms 2020, 8(12), 2031; https://doi.org/10.3390/microorganisms8122031 - 18 Dec 2020

Cited by 18 | Viewed by 4088

Abstract

Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) between people and pets, and their co-carriage, are well-described. Potential exchange of antimicrobial resistance (AMR) genes amongst these staphylococci was investigated in vitro through endogenous bacteriophage-mediated transduction. Bacteriophages were UV-induced from seven [...] Read more.

Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) between people and pets, and their co-carriage, are well-described. Potential exchange of antimicrobial resistance (AMR) genes amongst these staphylococci was investigated in vitro through endogenous bacteriophage-mediated transduction. Bacteriophages were UV-induced from seven donor isolates of canine (MRSP) and human (MRSA) origin, containing tet(M), tet(K), fusB or fusC, and lysates filtered. Twenty-seven tetracycline- and fusidic acid- (FA-) susceptible recipients were used in 122 donor-recipient combinations (22 tetracycline, 100 FA) across 415 assays (115 tetracycline, 300 FA). Bacteriophage lysates were incubated with recipients and presumed transductants quantified on antimicrobial-supplemented agar plates. Tetracycline resistance transduction from MRSP and MRSA to methicillin-susceptible S. pseudintermedius (MSSP) was confirmed by PCR in 15/115 assays. No FA-resistance transfer occurred, confirmed by negative fusB/fusC PCR, but colonies resulting from FA assays had high MICs (≥32 mg/L) and showed mutations in fusA, two at a novel position (F88L), nine at H457[Y/N/L]. Horizontal gene transfer of tetracycline-resistance confirms that resistance genes can be shared between coagulase-positive staphylococci from different hosts. Cross-species AMR transmission highlights the importance of good antimicrobial stewardship across humans and veterinary species to support One Health. Full article

(This article belongs to the Section Medical Microbiology)

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13 pages, 2344 KiB

Open AccessArticle

Genomic and Metabolic Insights into Two Novel Thiothrix Species from Enhanced Biological Phosphorus Removal Systems

by Andrey V. Mardanov, Eugeny V. Gruzdev, Dmitry D. Smolyakov, Tatyana S. Rudenko, Alexey V. Beletsky, Maria V. Gureeva, Nikita D. Markov, Yulia Yu. Berestovskaya, Nikolai V. Pimenov, Nikolai V. Ravin and Margarita Yu. Grabovich

Microorganisms 2020, 8(12), 2030; https://doi.org/10.3390/microorganisms8122030 - 18 Dec 2020

Cited by 14 | Viewed by 4775

Abstract

Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species [...] Read more.

Two metagenome-assembled genomes (MAGs), obtained from laboratory-scale enhanced biological phosphorus removal bioreactors, were analyzed. The values of 16S rRNA gene sequence identity, average nucleotide identity, and average amino acid identity indicated that these genomes, designated as RT and SSD2, represented two novel species within the genus Thiothrix, ‘Candidatus Thiothrix moscowensis’ and ‘Candidatus Thiothrix singaporensis’. A complete set of genes for the tricarboxylic acid cycle and electron transport chain indicates a respiratory type of metabolism. A notable feature of RT and SSD2, as well as other Thiothrix species, is the presence of a flavin adenine dinucleotide (FAD)-dependent malate:quinone oxidoreductase instead of nicotinamide adenine dinucleotide (NAD)-dependent malate dehydrogenase. Both MAGs contained genes for CO₂ assimilation through the Calvin–Benson–Bassam cycle; sulfide oxidation (sqr, fccAB), sulfur oxidation (rDsr complex), direct (soeABC) and indirect (aprBA, sat) sulfite oxidation, and the branched Sox pathway (SoxAXBYZ) of thiosulfate oxidation to sulfur and sulfate. All these features indicate a chemoorganoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic lifestyle. Both MAGs comprise genes for nitrate reductase and NO-reductase, while SSD2 also contains genes for nitrite reductase. The presence of polyphosphate kinase and exopolyphosphatase suggests that RT and SSD2 could accumulate and degrade polyhosphates during the oxic-anoxic growth cycle in the bioreactors, such as typical phosphate-accumulating microorganisms. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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23 pages, 4493 KiB

Open AccessArticle

Uncoupling Foam Fractionation and Foam Adsorption for Enhanced Biosurfactant Synthesis and Recovery

by Christian C. Blesken, Tessa Strümpfler, Till Tiso and Lars M. Blank

Microorganisms 2020, 8(12), 2029; https://doi.org/10.3390/microorganisms8122029 - 18 Dec 2020

Cited by 21 | Viewed by 3688

Abstract

The production of biosurfactants is often hampered by excessive foaming in the bioreactor, impacting system scale-up and downstream processing. Foam fractionation was proposed to tackle this challenge by combining in situ product removal with a pre-purification step. In previous studies, foam fractionation was [...] Read more.

The production of biosurfactants is often hampered by excessive foaming in the bioreactor, impacting system scale-up and downstream processing. Foam fractionation was proposed to tackle this challenge by combining in situ product removal with a pre-purification step. In previous studies, foam fractionation was coupled to bioreactor operation, hence it was operated at suboptimal parameters. Here, we use an external fractionation column to decouple biosurfactant production from foam fractionation, enabling continuous surfactant separation, which is especially suited for system scale-up. As a subsequent product recovery step, continuous foam adsorption was integrated into the process. The configuration is evaluated for rhamnolipid (RL) or 3-(3-hydroxyalkanoyloxy)alkanoic acid (HAA, i.e., RL precursor) production by recombinant non-pathogenic Pseudomonas putida KT2440. Surfactant concentrations of 7.5 g_RL/L and 2.0 g_HAA/L were obtained in the fractionated foam. 4.7 g RLs and 2.8 g HAAs could be separated in the 2-stage recovery process within 36 h from a 2 L culture volume. With a culture volume scale-up to 9 L, 16 g RLs were adsorbed, and the space-time yield (STY) increased by 31% to

{0.21 g}_{RL} / L \cdot h

. We demonstrate a well-performing process design for biosurfactant production and recovery as a contribution to a vital bioeconomy. Full article

(This article belongs to the Special Issue Microbial Biosurfactants)

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17 pages, 944 KiB

Open AccessArticle

Identification and Characterization of 33 Bacillus cereus sensu lato Isolates from Agricultural Fields from Eleven Widely Distributed Countries by Whole Genome Sequencing

by Athanasios Zervas, Marie Rønne Aggerbeck, Henrietta Allaga, Mustafa Güzel, Marc Hendriks, IIona Jonuškienė, Orsolya Kedves, Ayse Kupeli, Janja Lamovšek, Pascal Mülner, Denise Munday, Şahin Namli, Hilal Samut, Ružica Tomičić, Zorica Tomičić, Filiz Yeni, Raida Zribi Zghal, Xingchen Zhao, Vincent Sanchis-Borja and Niels Bohse Hendriksen

Microorganisms 2020, 8(12), 2028; https://doi.org/10.3390/microorganisms8122028 - 18 Dec 2020

Cited by 10 | Viewed by 4326

Abstract

The phylogeny, identification, and characterization of 33 B. cereus sensu lato isolates originating from 17 agricultural soils from 11 countries were analyzed on the basis of whole genome sequencing. Phylogenetic analyses revealed all isolates are divided into six groups, which follows the generally [...] Read more.

The phylogeny, identification, and characterization of 33 B. cereus sensu lato isolates originating from 17 agricultural soils from 11 countries were analyzed on the basis of whole genome sequencing. Phylogenetic analyses revealed all isolates are divided into six groups, which follows the generally accepted phylogenetic division of B. cereus sensu lato isolates. Four different identification methods resulted in a variation in the identity of the isolates, as none of the isolates were identified as the same species by all four methods—only the recent identification method proposed directly reflected the phylogeny of the isolates. This points to the importance of describing the basis and method used for the identification. The presence and percent identity of the protein product of 19 genes potentially involved in pathogenicity divided the 33 isolates into groups corresponding to phylogenetic division of the isolates. This suggests that different pathotypes exist and that it is possible to differentiate between them by comparing the percent identity of proteins potentially involved in pathogenicity. This also reveals that a basic link between phylogeny and pathogenicity is likely to exist. The geographical distribution of the isolates is not random: they are distributed in relation to their division into the six phylogenetic groups, which again relates to different ecotypes with different temperature growth ranges. This means that we find it easier to analyze and understand the results obtained from the 33 B. cereus sensu lato isolates in a phylogenetic, patho-type and ecotype-oriented context, than in a context based on uncertain identification at the species level. Full article

(This article belongs to the Special Issue Human Pathogens in Primary Production Systems)

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37 pages, 2579 KiB

Open AccessReview

Processing of Metals and Metalloids by Actinobacteria: Cell Resistance Mechanisms and Synthesis of Metal(loid)-Based Nanostructures

by Alessandro Presentato, Elena Piacenza, Raymond J. Turner, Davide Zannoni and Martina Cappelletti

Microorganisms 2020, 8(12), 2027; https://doi.org/10.3390/microorganisms8122027 - 18 Dec 2020

Cited by 36 | Viewed by 5019

Abstract

Metal(loid)s have a dual biological role as micronutrients and stress agents. A few geochemical and natural processes can cause their release in the environment, although most metal-contaminated sites derive from anthropogenic activities. Actinobacteria include high GC bacteria that inhabit a wide range of [...] Read more.

Metal(loid)s have a dual biological role as micronutrients and stress agents. A few geochemical and natural processes can cause their release in the environment, although most metal-contaminated sites derive from anthropogenic activities. Actinobacteria include high GC bacteria that inhabit a wide range of terrestrial and aquatic ecological niches, where they play essential roles in recycling or transforming organic and inorganic substances. The metal(loid) tolerance and/or resistance of several members of this phylum rely on mechanisms such as biosorption and extracellular sequestration by siderophores and extracellular polymeric substances (EPS), bioaccumulation, biotransformation, and metal efflux processes, which overall contribute to maintaining metal homeostasis. Considering the bioprocessing potential of metal(loid)s by Actinobacteria, the development of bioremediation strategies to reclaim metal-contaminated environments has gained scientific and economic interests. Moreover, the ability of Actinobacteria to produce nanoscale materials with intriguing physical-chemical and biological properties emphasizes the technological value of these biotic approaches. Given these premises, this review summarizes the strategies used by Actinobacteria to cope with metal(loid) toxicity and their undoubted role in bioremediation and bionanotechnology fields. Full article

(This article belongs to the Special Issue Microbial Responses to Metal Stress, Molecular Mechanisms, Challenges and Implications)

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10 pages, 237 KiB

Open AccessReview

Living with Legionella and Other Waterborne Pathogens

by Joseph O. Falkinham III

Microorganisms 2020, 8(12), 2026; https://doi.org/10.3390/microorganisms8122026 - 18 Dec 2020

Cited by 32 | Viewed by 4521

Abstract

Legionella spp. and other opportunistic premise plumbing pathogens (OPPPs), including Pseudomonas aeruginosa, Mycobacterium avium, Stenotrophomonas maltophilia, and Acinetobacter baumannii, are normal inhabitants of natural waters, drinking water distribution systems and premise plumbing. Thus, humans are regularly exposed to these [...] Read more.

Legionella spp. and other opportunistic premise plumbing pathogens (OPPPs), including Pseudomonas aeruginosa, Mycobacterium avium, Stenotrophomonas maltophilia, and Acinetobacter baumannii, are normal inhabitants of natural waters, drinking water distribution systems and premise plumbing. Thus, humans are regularly exposed to these pathogens. Unfortunately, Legionella spp. and the other OPPPs share a number of features that allow them to grow and persist in premise plumbing. They form biofilms and are also relatively disinfectant-resistant, able to grow at low organic matter concentrations, and able to grow under stagnant conditions. Infections have been traced to exposure to premise plumbing or aerosols generated in showers. A number of measures can lead to reduction in OPPP numbers in premise plumbing, including elevation of water heater temperatures. Full article

(This article belongs to the Special Issue Legionella and Legionnaires’ Disease: Pathogenesis, Prevention, and Public Health)

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