Microorganisms

19 pages, 2525 KiB

Open AccessEditor’s ChoiceArticle

Probiotic Alternative to Chlorhexidine in Periodontal Therapy: Evaluation of Clinical and Microbiological Parameters

by Andrea Butera, Simone Gallo, Carolina Maiorani, Domenico Molino, Alessandro Chiesa, Camilla Preda, Francesca Esposito and Andrea Scribante

Microorganisms 2021, 9(1), 69; https://doi.org/10.3390/microorganisms9010069 - 29 Dec 2020

Cited by 97 | Viewed by 6547

Abstract

Periodontitis consists of a progressive destruction of tooth-supporting tissues. Considering that probiotics are being proposed as a support to the gold standard treatment Scaling-and-Root-Planing (SRP), this study aims to assess two new formulations (toothpaste and chewing-gum). 60 patients were randomly assigned to three [...] Read more.

Periodontitis consists of a progressive destruction of tooth-supporting tissues. Considering that probiotics are being proposed as a support to the gold standard treatment Scaling-and-Root-Planing (SRP), this study aims to assess two new formulations (toothpaste and chewing-gum). 60 patients were randomly assigned to three domiciliary hygiene treatments: Group 1 (SRP + chlorhexidine-based toothpaste) (control), Group 2 (SRP + probiotics-based toothpaste) and Group 3 (SRP + probiotics-based toothpaste + probiotics-based chewing-gum). At baseline (T₀) and after 3 and 6 months (T₁–T₂), periodontal clinical parameters were recorded, along with microbiological ones by means of a commercial kit. As to the former, no significant differences were shown at T₁ or T₂, neither in controls for any index, nor in the experimental groups for adherent gingiva and gingival recession. Conversely, some significant differences were found in Group 2 and 3 for the other clinical indexes tested. Considering microbiological parameters, no significant differences were detected compared to baseline values for any group, except in Group 2 and 3 at T₂ only for the percentage of the orange complex pathogens and for the copies/microliter of Prevotella intermedia and Fusobacterium nucleatum. Accordingly, although colonization of probiotic bacteria has not been assessed in this study, the probiotics tested represent a valid support to SRP with a benefit on several clinical indexes and on specific periodontopathogens. Despite this promising action, the relationship between the use of probiotics and improvement in clinical parameters is still unclear and deserves to be further explored. Full article

(This article belongs to the Special Issue Oral Biofilms)

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19 pages, 1765 KiB

Open AccessEditor’s ChoiceArticle

Anti–SARS-CoV-2 Antibody Responses in Convalescent Plasma Donors Are Increased in Hospitalized Patients; Subanalyses of a Phase 2 Clinical Study

by Evangelos Terpos, Marianna Politou, Theodoros N. Sergentanis, Andreas Mentis, Margherita Rosati, Dimitris Stellas, Jenifer Bear, Xintao Hu, Barbara K. Felber, Vassiliki Pappa, Maria Pagoni, Elisavet Grouzi, Stavroula Labropoulou, Ioanna Charitaki, Ioannis Ntanasis-Stathopoulos, Dimitra Moschandreou, Anthi Bouhla, Stylianos Saridakis, Eleni Korompoki, Chara Giatra, Tina Bagratuni, Angelos Pefanis, Sotirios Papageorgiou, Alexandros Spyridonidis, Anastasia Antoniadou, Anastasia Kotanidou, Konstantinos Syrigos, Konstantinos Stamoulis, George Panayiotakopoulos, Sotirios Tsiodras, Leonidas Alexopoulos, Meletios A. Dimopoulos and George N. Pavlakis Show full author list Hide full author list

Microorganisms 2020, 8(12), 1885; https://doi.org/10.3390/microorganisms8121885 - 28 Nov 2020

Cited by 37 | Viewed by 5606

Abstract

We evaluated the antibody responses in 259 potential convalescent plasma donors for Covid-19 patients. Different assays were used: a commercial ELISA detecting antibodies against the recombinant spike protein (S1); a multiplex assay detecting total and specific antibody isotypes against three SARS-CoV-2 antigens (S1, [...] Read more.

We evaluated the antibody responses in 259 potential convalescent plasma donors for Covid-19 patients. Different assays were used: a commercial ELISA detecting antibodies against the recombinant spike protein (S1); a multiplex assay detecting total and specific antibody isotypes against three SARS-CoV-2 antigens (S1, basic nucleocapsid (N) protein and receptor-binding domain (RBD)); and an in-house ELISA detecting antibodies to complete spike, RBD and N in 60 of these donors. Neutralizing antibodies (NAb) were also evaluated in these 60 donors. Analyzed samples were collected at a median time of 62 (14–104) days from the day of first symptoms or positive PCR (for asymptomatic patients). Anti-SARS-CoV-2 antibodies were detected in 88% and 87.8% of donors using the ELISA and the multiplex assay, respectively. The multivariate analysis showed that age ≥50 years (p < 0.001) and need for hospitalization (p < 0.001) correlated with higher antibody titers, while asymptomatic status (p < 0.001) and testing >60 days after symptom onset (p = 0.001) correlated with lower titers. Interestingly, pseudotype virus-neutralizing antibodies (PsNAbs) significantly correlated with spike and with RBD antibodies by ELISA. Sera with high PsNAb also showed a strong ability to neutralize active SARS-CoV-2 virus, with hospitalized patients showing higher titers. Therefore, convalescent plasma donors can be selected based on the presence of high RBD antibody titers. Full article

(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)

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18 pages, 2010 KiB

Open AccessEditor’s ChoiceArticle

The Halotolerant Rhizobacterium—Pseudomonas koreensis MU2 Enhances Inorganic Silicon and Phosphorus Use Efficiency and Augments Salt Stress Tolerance in Soybean (Glycine max L.)

by Arjun Adhikari, Muhammad Aaqil Khan, Ko-Eun Lee, Sang-Mo Kang, Sanjeev Kumar Dhungana, Narayan Bhusal and In-Jung Lee

Microorganisms 2020, 8(9), 1256; https://doi.org/10.3390/microorganisms8091256 - 19 Aug 2020

Cited by 49 | Viewed by 5070

Abstract

Optimizing nutrient usage in plants is vital for a sustainable yield under biotic and abiotic stresses. Since silicon and phosphorus are considered key elements for plant growth, this study assessed the efficient supplementation strategy of silicon and phosphorus in soybean plants under salt [...] Read more.

Optimizing nutrient usage in plants is vital for a sustainable yield under biotic and abiotic stresses. Since silicon and phosphorus are considered key elements for plant growth, this study assessed the efficient supplementation strategy of silicon and phosphorus in soybean plants under salt stress through inoculation using the rhizospheric strain—Pseudomonas koreensis MU2. The screening analysis of MU2 showed its high salt-tolerant potential, which solubilizes both silicate and phosphate. The isolate, MU2 produced gibberellic acid (GA₁, GA₃) and organic acids (malic acid, citric acid, acetic acid, and tartaric acid) in pure culture under both normal and salt-stressed conditions. The combined application of MU2, silicon, and phosphorus significantly improved silicon and phosphorus uptake, reduced Na⁺ ion influx by 70%, and enhanced K⁺ uptake by 46% in the shoots of soybean plants grown under salt-stress conditions. MU2 inoculation upregulated the salt-resistant genes GmST1, GmSALT3, and GmAKT2, which significantly reduced the endogenous hormones abscisic acid and jasmonic acid while, it enhanced the salicylic acid content of soybean. In addition, MU2 inoculation strengthened the host’s antioxidant system through the reduction of lipid peroxidation and proline while, it enhanced the reduced glutathione content. Moreover, MU2 inoculation promoted root and shoot length, plant biomass, and the chlorophyll content of soybean plants. These findings suggest that MU2 could be a potential biofertilizer catalyst for the amplification of the use efficiency of silicon and phosphorus fertilizers to mitigate salt stress. Full article

(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion)

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7 pages, 766 KiB

Open AccessEditor’s ChoiceCommunication

Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm

by Alexandra Irrgang, Natalie Pauly, Bernd-Alois Tenhagen, Mirjam Grobbel, Annemarie Kaesbohrer and Jens A. Hammerl

Microorganisms 2020, 8(6), 855; https://doi.org/10.3390/microorganisms8060855 - 5 Jun 2020

Cited by 25 | Viewed by 3113

Abstract

Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans [...] Read more.

Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans to non-human reservoirs (i.e., environment, animals, food). In Germany, the occurrence of CPE in livestock and food has been systematically monitored since 2016. In the 2019 monitoring, an OXA-48-producing E. coli (19-AB01443) was recovered from a fecal sample of a fattening pig. Phenotypic resistance was confirmed by broth microdilution and further characterized by PFGE, conjugation, and combined short-/long-read whole genome sequencing. This is the first detection of this resistance determinant in samples from German meat production. Molecular characterization and whole-genome sequencing revealed that the bla_OXA-48 gene was located on a common pOXA-48 plasmid-prototype. This plasmid-type seems to be globally distributed among various bacterial species, but it was frequently associated with clinical Klebsiella spp. isolates. Currently, the route of introduction of this plasmid/isolate combination into the German pig production is unknown. We speculate that due to its strong correlation with human isolates a transmission from humans to livestock has occurred. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in the Food Production Chain )

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22 pages, 2075 KiB

Open AccessEditor’s ChoiceArticle

Effect of Co-Inoculation of Candida zemplinina, Saccharomyces cerevisiae and Lactobacillus plantarum for the Industrial Production of Negroamaro Wine in Apulia (Southern Italy)

by Maria Tufariello, Vittorio Capozzi, Giuseppe Spano, Giovanni Cantele, Pasquale Venerito, Giovanni Mita and Francesco Grieco

Microorganisms 2020, 8(5), 726; https://doi.org/10.3390/microorganisms8050726 - 13 May 2020

Cited by 33 | Viewed by 3494

Abstract

The employment of multi-species starter cultures has growing importance in modern winemaking for improving the complexity and wine attributes. The assessment of compatibility for selected species/strains at the industrial-scale is crucial to assure the quality and the safety associated with fermentations. An aspect [...] Read more.

The employment of multi-species starter cultures has growing importance in modern winemaking for improving the complexity and wine attributes. The assessment of compatibility for selected species/strains at the industrial-scale is crucial to assure the quality and the safety associated with fermentations. An aspect particularly relevant when the species belong to non-Saccharomyces, Saccharomyces spp. and malolactic bacteria, three categories with different biological characteristics and oenological significance. To the best of our knowledge, the present report is the first study regarding the utilization of a combined starter culture composed of three strains of non-Saccharomyces, Saccharomyces cerevisiae and Lactobacillus plantarum for production of wine at the industrial scale. More in-depth, this work investigated the oenological potential of the autochthonous characterized strains from the Apulian region (Southern Italy), Candida zemplinina (syn. Starmerella bacillaris) 35NC1, S. cerevisiae (NP103), and L. plantarum (LP44), in co-inoculation following a complete scale-up scheme. Microbial dynamics, fermentative profiles and production of volatile secondary compounds were assessed in lab-scale micro-vinification tests and then the performances of the mixed starter formulation were further evaluated by pilot-scale wine production. The above results were finally validated by performing an industrial-scale vinification on 100HL of Negroamaro cultivar grape must. The multi-starter formulation was able to rule the different stages of the fermentation processes effectively, and the different microbial combinations enhanced the organoleptic wine features to different extents. The findings indicated that the simultaneous inoculation of the three species affect the quality and quantity of several volatile compounds, confirming that the complexity of the wine can reflect the complexity of the starter cultures. Moreover, the results underlined that the same mixed culture could differently influence wine quality when tested at the lab-, pilot- and industrial-scale. Finally, we highlighted the significance of employment non-Saccharomyces and L. plantarum, together with S. cerevisiae, autochthonous strains in the design of custom-made starter culture formulation for typical regional wine production with pronounced unique quality. Full article

(This article belongs to the Special Issue Microbial Dynamics in Wine Production)

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18 pages, 4372 KiB

Open AccessEditor’s ChoiceArticle

Microbial Community and Fermentation Dynamics of Corn Silage Prepared with Heat-Resistant Lactic Acid Bacteria in a Hot Environment

by Hao Guan, Yang Shuai, Yanhong Yan, Qifan Ran, Xia Wang, Dandan Li, Yimin Cai and Xinquan Zhang

Microorganisms 2020, 8(5), 719; https://doi.org/10.3390/microorganisms8050719 - 12 May 2020

Cited by 49 | Viewed by 5269

Abstract

To develop a silage fermentation technique to adapt to global climate changes, the microbiome and fermentation dynamics of corn silage inoculated with heat-resistant lactic acid bacteria (LAB) under high-temperature conditions were studied. Corn was ensiled in laboratory silo, with and without two selected [...] Read more.

To develop a silage fermentation technique to adapt to global climate changes, the microbiome and fermentation dynamics of corn silage inoculated with heat-resistant lactic acid bacteria (LAB) under high-temperature conditions were studied. Corn was ensiled in laboratory silo, with and without two selected strains, Lactobacillus salivarius LS358 and L. rhamnosus LR753, two type strains L. salivarius ATCC 11741^T and L. rhamnosus ATCC 7469^T. The ensiling temperatures were designed at 30 °C and 45 °C, and the sampling took place after 0, 3, 7, 14, and 60 days of fermentation. The higher pH and dry matter losses were observed in the silages stored at 45 °C compared to those stored at 30 °C. Silages inoculated with strains LS358 and LR753 at 30 °C had a lower ratio of lactic acid/acetic acid. The dominant bacterial genera gradually changed from Pediococcus and Lactobacillus to Lactobacillus in silages during ensiling at 30 °C, while the bacterial community became more complex and fragmented after 7 d of ensiling at 45 °C. The high temperatures significantly led to a transformation of the LAB population from homo-fermentation to hetero-fermentation. This study is the first to describe microbial population dynamics response to high temperature during corn ensiling, and the results indicate that L. rhamnosus 753 shows potential ability to improve silage fermentation in tropics and subtropics. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria and Bifidobacteria and Their Application)

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12 pages, 822 KiB

Open AccessEditor’s ChoiceArticle

Tocilizumab for Treatment of Severe COVID-19 Patients: Preliminary Results from SMAtteo COvid19 REgistry (SMACORE)

by Marta Colaneri, Laura Bogliolo, Pietro Valsecchi, Paolo Sacchi, Valentina Zuccaro, Fabio Brandolino, Carlomaurizio Montecucco, Francesco Mojoli, Emanuele Maria Giusti, Raffaele Bruno and the COVID IRCCS San Matteo Pavia Task Force

Microorganisms 2020, 8(5), 695; https://doi.org/10.3390/microorganisms8050695 - 9 May 2020

Cited by 169 | Viewed by 14142

Abstract

Objective: This study aimed to assess the role of Tocilizumab therapy (TCZ) in terms of ICU admission and mortality rate of critically ill patients with severe COVID-19 pneumonia. Design: Patients with COVID-19 pneumonia were prospectively enrolled in SMAtteo COvid19 REgistry (SMACORE). A retrospective [...] Read more.

Objective: This study aimed to assess the role of Tocilizumab therapy (TCZ) in terms of ICU admission and mortality rate of critically ill patients with severe COVID-19 pneumonia. Design: Patients with COVID-19 pneumonia were prospectively enrolled in SMAtteo COvid19 REgistry (SMACORE). A retrospective analysis of patients treated with TCZ matched using propensity score to patients treated with Standard Of Care (SOC) was conducted. Setting: The study was conducted at IRCCS Policlinico San Matteo Hospital, Pavia, Italy, from March 14, 2020 to March 27, 2020. Participants: Patients with a confirmed diagnosis of COVID-19 hospitalized in our institution at the time of TCZ availability. Interventions: TCZ was administered to 21 patients. The first administration was 8 mg/kg (up to a maximum 800 mg per dose) of Tocilizumab intravenously, repeated after 12 h if no side effects were reported after the first dose. Main Outcomes and Measures: ICU admission and 7-day mortality rate. Secondary outcomes included clinical and laboratory data. Results: There were 112 patients evaluated (82 were male and 30 were female, with a median age of 63.55 years). Using propensity scores, the 21 patients who received TCZ were matched to 21 patients who received SOC (a combination of hydroxychloroquine, azithromycin and prophylactic dose of low weight heparin). No adverse event was detected following TCZ administration. This study found that treatment with TCZ did not significantly affect ICU admission (OR 0.11; 95% CI between 0.00 and 3.38; p = 0.22) or 7-day mortality rate (OR 0.78; 95% CI between 0.06 and 9.34; p = 0.84) when compared with SOC. Analysis of laboratory measures showed significant interactions between time and treatment regarding C-Reactive Protein (CRP), alanine aminotransferase (ALT), platelets and international normalized ratio (INR) levels. Variation in lymphocytes count was observed over time, irrespective of treatment. Conclusions: TCZ administration did not reduce ICU admission or mortality rate in a cohort of 21 patients. Additional data are needed to understand the effect(s) of TCZ in treating patients diagnosed with COVID-19. Full article

(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)

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18 pages, 2180 KiB

Open AccessEditor’s ChoiceArticle

Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH

by Washington Logroño, Denny Popp, Sabine Kleinsteuber, Heike Sträuber, Hauke Harms and Marcell Nikolausz

Microorganisms 2020, 8(4), 614; https://doi.org/10.3390/microorganisms8040614 - 24 Apr 2020

Cited by 44 | Viewed by 5585

Abstract

Biomethanation is a promising solution to convert H₂ (produced from surplus electricity) and CO₂ to CH₄ by using hydrogenotrophic methanogens. In ex situ biomethanation with mixed cultures, homoacetogens and methanogens compete for H₂/CO₂. We enriched a [...] Read more.

Biomethanation is a promising solution to convert H₂ (produced from surplus electricity) and CO₂ to CH₄ by using hydrogenotrophic methanogens. In ex situ biomethanation with mixed cultures, homoacetogens and methanogens compete for H₂/CO₂. We enriched a hydrogenotrophic microbiota on CO₂ and H₂ as sole carbon and energy sources, respectively, to investigate these competing reactions. The microbial community structure and dynamics of bacteria and methanogenic archaea were evaluated through 16S rRNA and mcrA gene amplicon sequencing, respectively. Hydrogenotrophic methanogens and homoacetogens were enriched, as acetate was concomitantly produced alongside CH₄. By controlling the media composition, especially changing the reducing agent, the formation of acetate was lowered and grid quality CH₄ (≥97%) was obtained. Formate was identified as an intermediate that was produced and consumed during the bioprocess. Stirring intensities ≥ 1000 rpm were detrimental, probably due to shear force stress. The predominating methanogens belonged to the genera Methanobacterium and Methanoculleus. The bacterial community was dominated by Lutispora. The methanogenic community was stable, whereas the bacterial community was more dynamic. Our results suggest that hydrogenotrophic communities can be steered towards the selective production of CH₄ from H₂/CO₂ by adapting the media composition, the reducing agent and the stirring intensity. Full article

(This article belongs to the Special Issue Anaerobic Digestion)

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18 pages, 2644 KiB

Open AccessEditor’s ChoiceCommunication

The Microbiota–Gut–Brain Axis–Heart Shunt Part II: Prosaic Foods and the Brain–Heart Connection in Alzheimer Disease

by Mark Obrenovich, Shams Tabrez, Bushra Siddiqui, Benjamin McCloskey and George Perry

Microorganisms 2020, 8(4), 493; https://doi.org/10.3390/microorganisms8040493 - 31 Mar 2020

Cited by 22 | Viewed by 7349

Abstract

There is a strong cerebrovascular component to brain aging, Alzheimer disease, and vascular dementia. Foods, common drugs, and the polyphenolic compounds contained in wine modulate health both directly and through the gut microbiota. This observation and novel findings centered on nutrition, biochemistry, and [...] Read more.

There is a strong cerebrovascular component to brain aging, Alzheimer disease, and vascular dementia. Foods, common drugs, and the polyphenolic compounds contained in wine modulate health both directly and through the gut microbiota. This observation and novel findings centered on nutrition, biochemistry, and metabolism, as well as the newer insights we gain into the microbiota-gut-brain axis, now lead us to propose a shunt to this classic triad, which involves the heart and cerebrovascular systems. The French paradox and prosaic foods, as they relate to the microbiota-gut-brain axis and neurodegenerative diseases, are discussed in this manuscript, which is the second part of a two-part series of concept papers addressing the notion that the microbiota and host liver metabolism all play roles in brain and heart health. Full article

(This article belongs to the Special Issue Microbiota-Gut-Brain Axis)

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15 pages, 2649 KiB

Open AccessEditor’s ChoiceArticle

Antimicrobial and Fermentation Potential of Himanthalia elongata in Food Applications

by Francesco Martelli, Claudia Favari, Pedro Mena, Stefano Guazzetti, Annalisa Ricci, Daniele Del Rio, Camilla Lazzi, Erasmo Neviani and Valentina Bernini

Microorganisms 2020, 8(2), 248; https://doi.org/10.3390/microorganisms8020248 - 13 Feb 2020

Cited by 25 | Viewed by 4517

Abstract

Himanthalia elongata is a brown oceanic seaweed rich in bioactive compounds. It could play an important role in food production because of its antimicrobial and antioxidant properties. Three strains belonging to the Lactobacillus casei group (Lactobacillus casei, Lactobacillus paracasei, and [...] Read more.

Himanthalia elongata is a brown oceanic seaweed rich in bioactive compounds. It could play an important role in food production because of its antimicrobial and antioxidant properties. Three strains belonging to the Lactobacillus casei group (Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus) and a Bacillus subtilis strain were used for the solid-state fermentation of commercial seaweeds, and bacterial growth was monitored using the plate count method. High-pressure processing (HPP) was also employed (6000 bar, 5 min, 5 °C) before extraction. The antimicrobial activity of the extracts was tested in terms of the main food pathogenic bacteria (Salmonella spp., Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, and Bacillus cereus), and the phenolic content was estimated using the Folin–Ciocalteau method. In addition, targeted UHPLC-MS² methods were used to unravel the profile of phlorotannins. H. elongata allowed the growth of the L. casei group strains and B. subtilis, showing the fermentability of this substrate. Significant antimicrobial activity toward L. monocytogenes was observed in the extracts obtained from unfermented samples, but neither fermentation nor HPP enhanced the natural antimicrobial activity of this seaweed species. The content in the phenolic compounds decreased because of the fermentation process, and the amount of phenolics in both the unfermented and fermented H. elongata extracts was very low. Despite phlorotannins being related to the natural antimicrobial activity of this brown seaweed, these results did not support this association. Even if fermentation and HPP were not proven to be effective tools for enhancing the useful compounds of H. elongata, the seaweed was shown to be a suitable substrate for L. casei group strains as well as for B. subtilis growth, and its extracts exhibited antimicrobial activity toward foodborne pathogens. Full article

(This article belongs to the Special Issue Biocontrol of Food Borne Pathogens)

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17 pages, 1584 KiB

Open AccessEditor’s ChoiceArticle

Genome Sequencing of Pantoea agglomerans C1 Provides Insights into Molecular and Genetic Mechanisms of Plant Growth-Promotion and Tolerance to Heavy Metals

by Francesca Luziatelli, Anna Grazia Ficca, Mariateresa Cardarelli, Francesca Melini, Andrea Cavalieri and Maurizio Ruzzi

Microorganisms 2020, 8(2), 153; https://doi.org/10.3390/microorganisms8020153 - 22 Jan 2020

Cited by 43 | Viewed by 4862

Abstract

Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. [...] Read more.

Distinctive strains of Pantoea are used as soil inoculants for their ability to promote plant growth. Pantoea agglomerans strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as Erwinia amylovora. In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils. Full article

(This article belongs to the Section Plant Microbe Interactions)

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11 pages, 11593 KiB

Open AccessEditor’s ChoiceArticle

The Impact of Primer Design on Amplicon-Based Metagenomic Profiling Accuracy: Detailed Insights into Bifidobacterial Community Structure

by Leonardo Mancabelli, Christian Milani, Gabriele Andrea Lugli, Federico Fontana, Francesca Turroni, Douwe van Sinderen and Marco Ventura

Microorganisms 2020, 8(1), 131; https://doi.org/10.3390/microorganisms8010131 - 17 Jan 2020

Cited by 28 | Viewed by 4879

Abstract

Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological [...] Read more.

Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological processes important for preservation of the health status of the host. The most widespread microbiota profiling method is based on amplification and sequencing of a variable portion of the 16S rRNA gene as a universal taxonomic marker among members of the Bacteria domain. Despite its popularity and obvious advantages, this 16S rRNA gene-based approach comes with some important limitations. In particular, the choice of the primer pair for amplification plays a major role in defining the accuracy of the reconstructed bacterial profiles. In the current study, we performed an in silico PCR using all currently described 16S rRNA gene-targeting primer pairs (PP) in order to assess their efficiency. Our results show that V3, V4, V5, and V6 were the optimal regions on which to design 16S rRNA metagenomic primers. In detail, PP39 (Probio_Uni/Probio_Rev), PP41 (341F/534R), and PP72 (970F/1050R) were the most suitable primer pairs with an amplification efficiency of >98.5%. Furthermore, the Bifidobacterium genus was examined as a test case for accurate evaluation of intra-genus performances at subspecies level. Intriguingly, the in silico analysis revealed that primer pair PP55 (527f/1406r) was unable to amplify the targeted region of any member of this bacterial genus, while several other primer pairs seem to rather inefficiently amplify the target region of the main bifidobacterial taxa. These results highlight that selection of a 16S rRNA gene-based PP should be done with utmost care in order to avoid biases in microbiota profiling results. Full article

(This article belongs to the Special Issue Bifidobacteria: Insights from Ecology to Genomics of a Key Microbial Group of the Mammalian Gut Microbiota)

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