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Ridley RS, Conrad RE, Lindner BG, Woo S, Konstantinidis KT. Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes. Sci Rep 2024; 14:8798. [PMID: 38627476 PMCID: PMC11021508 DOI: 10.1038/s41598-024-59279-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.
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Affiliation(s)
- Rodney S Ridley
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Seongwook Woo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Schwarzerova J, Zeman M, Babak V, Jureckova K, Nykrynova M, Varga M, Weckwerth W, Dolejska M, Provaznik V, Rychlik I, Cejkova D. Detecting horizontal gene transfer among microbiota: an innovative pipeline for identifying co-shared genes within the mobilome through advanced comparative analysis. Microbiol Spectr 2024; 12:e0196423. [PMID: 38099617 PMCID: PMC10782964 DOI: 10.1128/spectrum.01964-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/31/2023] [Indexed: 01/13/2024] Open
Abstract
Horizontal gene transfer (HGT) is a key driver in the evolution of bacterial genomes. The acquisition of genes mediated by HGT may enable bacteria to adapt to ever-changing environmental conditions. Long-term application of antibiotics in intensive agriculture is associated with the dissemination of antibiotic resistance genes among bacteria with the consequences causing public health concern. Commensal farm-animal-associated gut microbiota are considered the reservoir of the resistance genes. Therefore, in this study, we identified known and not-yet characterized mobilized genes originating from chicken and porcine fecal samples using our innovative pipeline followed by network analysis to provide appropriate visualization to support proper interpretation.
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Affiliation(s)
- Jana Schwarzerova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michal Zeman
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Marketa Nykrynova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
| | - Margaret Varga
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Valentine Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
- Department of Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Brno, Czech Republic
| | - Darina Cejkova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czech Republic
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Chávez-Hernández M, Ortiz-Álvarez J, Morales-Jiménez J, Villa-Tanaca L, Hernández-Rodríguez C. Phenotypic and Genomic Characterization of Streptomyces pakalii sp. nov., a Novel Species with Anti-Biofilm and Anti-Quorum Sensing Activity in ESKAPE Bacteria. Microorganisms 2023; 11:2551. [PMID: 37894209 PMCID: PMC10608816 DOI: 10.3390/microorganisms11102551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The increasing number of infections caused by antimicrobial multi-resistant microorganisms has led to the search for new microorganisms capable of producing novel antibiotics. This work proposes Streptomyces pakalii sp. nov. as a new member of the Streptomycetaceae family. The strain ENCB-J15 was isolated from the jungle soil in Palenque National Park, Chiapas, Mexico. The strain formed pale brown, dry, tough, and buried colonies in the agar with no diffusible pigment in GAE (glucose-asparagine-yeast extract) medium. Scanning electron micrographs showed typical mycelium with long chains of smooth and oval-shaped spores (3-10 m). The strain grew in all of the International Streptomyces Project (ISP)'s media at 28-37 °C with a pH of 6-9 and 0-10% NaCl. S. pakalii ENCB-J15 assimilated diverse carbon as well as organic and inorganic nitrogen sources. The strain also exhibited significant inhibitory activity against the prodigiosin synthesis of Serratia marcescens and the inhibition of the formation and destruction of biofilms of ESKAPE strains of Acinetobacter baumannii and Klebsiella pneumoniae. The draft genome sequencing of ENCB-J15 revealed a 7.6 Mb genome with a high G + C content (71.6%), 6833 total genes, and 6746 genes encoding putative proteins. A total of 26 accessory clusters of proteins associated with carbon sources and amino acid catabolism, DNA modification, and the antibiotic biosynthetic process were annotated. The 16S rRNA gene phylogeny, core-proteome phylogenomic tree, and virtual genome fingerprints support that S. pakalii ENCB-J15 is a new species related to Streptomyces badius and Streptomyces globisporus. Similarly, its average nucleotide identity (ANI) (96.4%), average amino acid identity (AAI) (96.06%), and virtual DNA-DNA hybridization (67.3%) provide evidence to recognize it as a new species. Comparative genomics revealed that S. pakalli and its closest related species maintain a well-conserved genomic synteny. This work proposes Streptomyces pakalii sp. nov. as a novel species that expresses anti-biofilm and anti-quorum sensing activities.
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Affiliation(s)
- Michelle Chávez-Hernández
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - Jossue Ortiz-Álvarez
- Programa “Investigadoras e Investigadores por México”. Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT). Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México 03940, Mexico;
| | - Jesús Morales-Jiménez
- Departamento el Hombre y su Ambiente, Universidad Autónoma Metropolitana-Xochimilco, Calzada del Hueso 1100, Villa Quietud, Coyoacán, Ciudad de México 04960, Mexico;
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
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Pan P, Gu Y, Sun DL, Wu QL, Zhou NY. Microbial Diversity Biased Estimation Caused by Intragenomic Heterogeneity and Interspecific Conservation of 16S rRNA Genes. Appl Environ Microbiol 2023; 89:e0210822. [PMID: 37129483 PMCID: PMC10231250 DOI: 10.1128/aem.02108-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/09/2023] [Indexed: 05/03/2023] Open
Abstract
The 16S rRNA gene has been extensively used as a molecular marker to explore evolutionary relationships and profile microbial composition throughout various environments. Despite its convenience and prevalence, limitations are inevitable. Variable copy numbers, intragenomic heterogeneity, and low taxonomic resolution have caused biases in estimating microbial diversity. Here, analysis of 24,248 complete prokaryotic genomes indicated that the 16S rRNA gene copy number ranged from 1 to 37 in bacteria and 1 to 5 in archaea, and intragenomic heterogeneity was observed in 60% of prokaryotic genomes, most of which were below 1%. The overestimation of microbial diversity caused by intragenomic variation and the underestimation introduced by interspecific conservation were calculated when using full-length or partial 16S rRNA genes. Results showed that, at the 100% threshold, microbial diversity could be overestimated by as much as 156.5% when using the full-length gene. The V4 to V5 region-based analyses introduced the lowest overestimation rate (4.4%) but exhibited slightly lower species resolution than other variable regions under the 97% threshold. For different variable regions, appropriate thresholds rather than the canonical value 97% were proposed for minimizing the risk of splitting a single genome into multiple clusters and lumping together different species into the same cluster. This study has not only updated the 16S rRNA gene copy number and intragenomic variation information for the currently available prokaryotic genomes, but also elucidated the biases in estimating prokaryotic diversity with quantitative data, providing references for choosing amplified regions and clustering thresholds in microbial community surveys. IMPORTANCE Microbial diversity is typically analyzed using marker gene-based methods, of which 16S rRNA gene sequencing is the most widely used approach. However, obtaining an accurate estimation of microbial diversity remains a challenge, due to the intragenomic variation and low taxonomic resolution of 16S rRNA genes. Comprehensive examination of the bias in estimating such prokaryotic diversity using 16S rRNA genes within ever-increasing prokaryotic genomes highlights the importance of the choice of sequencing regions and clustering thresholds based on the specific research objectives.
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Affiliation(s)
- Piaopiao Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yichao Gu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Lei Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qinglong L. Wu
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Todorović I, Abrouk D, Kyselková M, Lavire C, Rey M, Raičević V, Jovičić-Petrović J, Moënne-Loccoz Y, Muller D. Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov. Syst Appl Microbiol 2023; 46:126425. [PMID: 37146562 DOI: 10.1016/j.syapm.2023.126425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/08/2023] [Accepted: 04/23/2023] [Indexed: 05/07/2023]
Abstract
Pseudomonas strains IT-194P, IT-215P, IT-P366T and IT-P374T were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366T and IT-194P and clustering (whole genome analysis) next to P. umsongensis DSM16611T, and another species containing strains IT-P374T and IT-215P and clustering next to P. koreensis LMG21318T. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366T (compared with P. umsongensis DSM16611T) and IT-P374T (compared with P. koreensis LMG21318T). Unlike P. umsongensis DSM16611T, strains of P. serbica can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to P. koreensis LMG21318T, strains of P. serboccidentalis can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names Pseudomonas serbica sp. nov., with the type strain IT-P366T (=CFBP 9060 T = LMG 32732 T = EML 1791 T) and Pseudomonas serboccidentalis sp. nov., with the type strain IT-P374T (=CFBP 9061 T = LMG 32734 T = EML 1792 T). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).
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Affiliation(s)
- Irena Todorović
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France; University of Belgrade, Faculty of Agriculture, Department of Microbial Ecology, Nemanjina 6, 11080 Zemun, Belgrade, Serbia
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Martina Kyselková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Céline Lavire
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Marjolaine Rey
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Vera Raičević
- University of Belgrade, Faculty of Agriculture, Department of Microbial Ecology, Nemanjina 6, 11080 Zemun, Belgrade, Serbia
| | - Jelena Jovičić-Petrović
- University of Belgrade, Faculty of Agriculture, Department of Microbial Ecology, Nemanjina 6, 11080 Zemun, Belgrade, Serbia
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
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Cai H, McLimans CJ, Beyer JE, Krumholz LR, Hambright KD. Microcystis pangenome reveals cryptic diversity within and across morphospecies. SCIENCE ADVANCES 2023; 9:eadd3783. [PMID: 36638170 PMCID: PMC9839332 DOI: 10.1126/sciadv.add3783] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.
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Affiliation(s)
- Haiyuan Cai
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Christopher J. McLimans
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Jessica E. Beyer
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Lee R. Krumholz
- Department of Microbiology and Plant Biology and Institute for Energy and the Environment, University of Oklahoma, Norman, OK, USA
| | - K. David Hambright
- Plankton Ecology and Limnology Laboratory, Department of Biology, University of Oklahoma, Norman, OK, USA
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, USA
- Geographical Ecology, Department of Biology, University of Oklahoma, Norman, OK, USA
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Musser E, Smith C, Halse TA, Kohlerschmidt D, Rourke A, Fiero A, Musser KA, Escuyer V, Lapierre P. Characterization of Mycobacterium salfingeri sp. nov.: A novel nontuberculous mycobacteria isolated from a human wound infection. Front Microbiol 2022; 13:992610. [PMID: 36299734 PMCID: PMC9589434 DOI: 10.3389/fmicb.2022.992610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental bacteria commonly found in soil and water in almost every part of the world. While usually non-pathogenic, they can cause acute respiratory and cutaneous infections under certain circumstances or in patients with underlying medical conditions. Contrary to members of the Mycobacterium tuberculosis complex, documented human-to-human transmissions of NTM have been rarely reported and most cases result from direct environmental exposure. Here we describe the identification of a new NTM species isolated from a hand laceration of a New York State patient after a fall. This new NTM forms rough, orange pigmented colonies and is naturally resistant to doxycycline and tobramycin. Whole genome analysis reveal no close relatives present in public databases, and our findings are in accordance with the recognition of a new taxonomic species of NTM. We propose the name Mycobacterium salfingeri sp. nov. for this new NTM representative. The type strain is 20-157661T (DSM = 113368T, BCCM = ITM 501207T).
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A culture-based and culture-independent approach to the study of landfill leachate bacterial and archaeal communities. Anaerobe 2022; 77:102626. [PMID: 35977655 DOI: 10.1016/j.anaerobe.2022.102626] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/14/2022] [Accepted: 08/09/2022] [Indexed: 11/20/2022]
Abstract
The landfill is a convenient and affordable method of municipal solid waste (MSW) management. Landfill leachate contains a heavy load of pollutants and pathogens. Discharge of untreated leachate is the leading cause of surface and groundwater contamination and a threat to public and environmental health. To develop an efficient leachate treatment technology, an in-depth understanding of landfill chemistry and microbiology is essential. In the present manuscript, we conducted a comparative study of three different landfill leachate samples using cultivation-based and culture-independent molecular studies. We cultivated 85 species of aerobic, anaerobic bacteria and archaea from leachate represented by a total of 200 strains using extensive culturomics approaches. Twelve out of 200 cultivated strains of bacteria showed very low 16S rRNA gene sequence similarity (84-98.6%) with their closest relatives and could be the potential novel taxa, the first time cultivated from leachate. Members of the six genera only have 2-5 representatives from past studies from other habitats but first time cultivated from leachate. In addition to bacteria, we also cultivated and characterized different groups of methanogenic archaea. Our chemistry data indicate that leachate is a highly stressed ecosystem with an assemblage of many toxic wastes like sulfur, zinc, mercury, chromium, etc. 16S rRNA gene-based amplicon analysis showed the dominance of (30-55%) methanogens and haloarachaea. Our data suggest that archaea are the significant regulators of leachate ecology, and more in-depth studies with multiple leachate samples are required to understand their role in leachate nutrient cycling and the development of effective leachate treatment technology.
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Sharma A, Sharma N, Gupta D, Lee HJ, Park YS. Comparative genome analysis of four Leuconostoc strains with a focus on carbohydrate-active enzymes and oligosaccharide utilization pathways. Comput Struct Biotechnol J 2022; 20:4771-4785. [PMID: 36147676 PMCID: PMC9465122 DOI: 10.1016/j.csbj.2022.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/30/2022] [Accepted: 08/13/2022] [Indexed: 11/03/2022] Open
Abstract
Comparative genomic analysis of four Leuconostoc strains was performed. Leuconostoc spp. shared genomic similarity, but their genetic content differed. Leuconostoc spp. showed different genes encoding CAZymes. Oligosaccharide’s utilization and folate biosynthesis pathways were investigated.
Leuconostoc is mostly found in food, plants, and dairy products. Due to their innate genomic features, such as the presence of carbohydrate-active enzymes, bacteriocins, and plasmids, Leuconostoc spp. have great biotechnological potential. In this study, four strains were isolated and identified as Leuconostoc mesenteroides SG315 (LA), L. citreum SG255 (LB), L. lactis CCK940 (LC), and L. lactis SBC001 (LD). Comparative analysis was performed using their draft genome sequences. Differences among the four strains were analyzed using the average nucleotide identity, dot plot, and multiple alignments of conserved genomic sequences. Functional profiling revealed 2134, 1917, 1751, and 1816 open reading frames; 2023, 1823, 1655, and 1699 protein-coding genes; 60, 57, 83, and 82 RNA-coding genes; and GC content of 37.5 %, 38.8 %, 43.3 %, and 43.2 %, in LA, LB, LC, and LD, respectively. The total number of genes encoding carbohydrate-active enzymes was 76 (LA), 73 (LB), 57 (LC), and 67 (LD). These results indicate that the four strains shared a large number of genes, but their gene content is different. Furthermore, most genes with unknown functions were observed in the prophage regions of the genome. This study also elucidated the oligosaccharide utilization and folate biosynthesis pathways in Leuconostoc spp. Taken together, our findings provide useful information on the genomic diversity of CAZymes in the four Leuconostoc strains and suggest that these species could be used for potent exploitation.
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Huang S, Zhang C, Xu T, Shaukat A, He Y, Chen P, Lin L, Yue K, Cao Q, Tong X. Integrated Fecal Microbiome and Metabolomics Reveals a Novel Potential Biomarker for Predicting Tibial Dyschondroplasia in Chickens. Front Physiol 2022; 13:887207. [PMID: 35634144 PMCID: PMC9133743 DOI: 10.3389/fphys.2022.887207] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Tibial dyschondroplasia (TD) is a metabolic tibial-tarsal disorder occurring in fast-growing poultry, and its diagnosis is mainly based on an invasive method. Here, we profiled the fecal gut microbiome and metabolome of broilers with and without TD to identify potential non-invasive and non-stress biomarkers of TD. First, TD broilers with the most pronounced clinical signs during the experiment were screened and faecal samples were collected for integrated microbiome and metabolomics analysis. Moreover, the diagnostic potential of identified biomarkers was further validated throughout the experiment. It was noted that the microbial and metabolic signatures of TD broilers differed from those of normal broilers. TD broilers were characterized by enriched bacterial OTUs of the genus Klebsiella, and depleted genera [Ruminococcus], Dorea, Ruminococcus, Oscillospira, Ochrobactrum, and Sediminibacterium. In addition, a total of 189 fecal differential metabolites were identified, mainly enriched in the purine, vitamin and amino acid metabolism, which were closely associated with differential microbiota and tibia-related indicators. Furthermore, three fecal metabolites were screened, including 4-hydroxybenzaldehyde, which distinguished TD from normal broilers with extremely high specificity and was superior to serum bone markers. These results indicated that gut microbiota equilibrium might influence the pathogenesis of TD by modulating host metabolism, and the identified fecal metabolite 4-hydroxybenzaldehyde might be a potential and non-invasive biomarker for predicting TD in chickens.
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Affiliation(s)
- Shucheng Huang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Shucheng Huang,
| | - Chaodong Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tingting Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Aftab Shaukat
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong Agricultural University, Wuhan, China
| | - Yanfeng He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Pan Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Luxi Lin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ke Yue
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qinqin Cao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xishuai Tong
- Institutes of Agricultural Science and Technology Development (Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China)/College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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11
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Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, Garcia SL. A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Front Microbiol 2022; 12:761869. [PMID: 35069467 PMCID: PMC8767057 DOI: 10.3389/fmicb.2021.761869] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/15/2021] [Indexed: 01/09/2023] Open
Abstract
Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Julia K. Nuy
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Sarahi L. Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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12
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Tee HS, Wood SA, Bouma-Gregson K, Lear G, Handley KM. Genome Streamlining, Plasticity, and Metabolic Versatility Distinguish Co-occurring Toxic and Nontoxic Cyanobacterial Strains of Microcoleus. mBio 2021; 12:e0223521. [PMID: 34700377 PMCID: PMC8546630 DOI: 10.1128/mbio.02235-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 01/21/2023] Open
Abstract
Harmful cyanobacterial bloom occurrences have increased worldwide due to climate change and eutrophication, causing nuisance and animal deaths. Species from the benthic cyanobacterial genus Microcoleus are ubiquitous and form thick mats in freshwater systems, such as rivers, that are sometimes toxic due to the production of potent neurotoxins (anatoxins). Anatoxin-producing (toxic) strains typically coexist with non-anatoxin-producing (nontoxic) strains in mats, although the reason for this is unclear. To determine the genetic mechanisms differentiating toxic and nontoxic Microcoleus, we sequenced and assembled genomes from 11 cultures and compared these to another 31 Microcoleus genomes. Average nucleotide identities (ANI) indicate that toxic and nontoxic strains are distinct species (ANI, <95%), and only 6% of genes are shared across all 42 genomes, suggesting a high level of genetic divergence among Microcoleus strains. Comparative genomics showed substantial genome streamlining in toxic strains and a potential dependency on external sources for thiamine and sucrose. Toxic and nontoxic strains are further differentiated by an additional set of putative nitrate transporter (nitrogen uptake) and cyanophycin (carbon and nitrogen storage) genes, respectively. These genes likely confer distinct competitive advantages based on nutrient availability and suggest nontoxic strains are more robust to nutrient fluctuations. Nontoxic strains also possess twice as many transposable elements, potentially facilitating greater genetic adaptation to environmental changes. Our results offer insights into the divergent evolution of Microcoleus strains and the potential for cooperative and competitive interactions that contribute to the co-occurrence of toxic and nontoxic species within mats. IMPORTANCE Microcoleus autumnalis, and closely related Microcoleus species, compose a geographically widespread group of freshwater benthic cyanobacteria. Canine deaths due to anatoxin-a poisoning, following exposure to toxic proliferations, have been reported globally. While Microcoleus proliferations are on the rise, the mechanisms underpinning competition between, or coexistence of, toxic and nontoxic strains are unknown. This study identifies substantial genetic differences between anatoxin-producing and non-anatoxin-producing strains, pointing to reduced metabolic flexibility in toxic strains, and potential dependence on cohabiting nontoxic strains. Results provide insights into the metabolic and evolutionary differences between toxic and nontoxic Microcoleus, which may assist in predicting and managing aquatic proliferations.
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Affiliation(s)
- Hwee Sze Tee
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Keith Bouma-Gregson
- U.S. Geological Survey, California Water Science Center, Sacramento, California, USA
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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13
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Abstract
Amplicon sequencing variants (ASVs) have been proposed as an alternative to operational taxonomic units (OTUs) for analyzing microbial communities. ASVs have grown in popularity, in part because of a desire to reflect a more refined level of taxonomy since they do not cluster sequences based on a distance-based threshold. However, ASVs and the use of overly narrow thresholds to identify OTUs increase the risk of splitting a single genome into separate clusters. To assess this risk, I analyzed the intragenomic variation of 16S rRNA genes from the bacterial genomes represented in an rrn copy number database, which contained 20,427 genomes from 5,972 species. As the number of copies of the 16S rRNA gene increased in a genome, the number of ASVs also increased. There was an average of 0.58 ASVs per copy of the 16S rRNA gene for full-length 16S rRNA genes. It was necessary to use a distance threshold of 5.25% to cluster full-length ASVs from the same genome into a single OTU with 95% confidence for genomes with 7 copies of the 16S rRNA, such as Escherichia coli. This research highlights the risk of splitting a single bacterial genome into separate clusters when ASVs are used to analyze 16S rRNA gene sequence data. Although there is also a risk of clustering ASVs from different species into the same OTU when using broad distance thresholds, these risks are of less concern than artificially splitting a genome into separate ASVs and OTUs. IMPORTANCE 16S rRNA gene sequencing has engendered significant interest in studying microbial communities. There has been tension between trying to classify 16S rRNA gene sequences to increasingly lower taxonomic levels and the reality that those levels were defined using more sequence and physiological information than is available from a fragment of the 16S rRNA gene. Furthermore, the naming of bacterial taxa reflects the biases of those who name them. One motivation for the recent push to adopt ASVs in place of OTUs in microbial community analyses is to allow researchers to perform their analyses at the finest possible level that reflects species-level taxonomy. The current research is significant because it quantifies the risk of artificially splitting bacterial genomes into separate clusters. Far from providing a better representation of bacterial taxonomy and biology, the ASV approach can lead to conflicting inferences about the ecology of different ASVs from the same genome.
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14
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Satti SM, Castro-Aguirre E, Shah AA, Marsh TL, Auras R. Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp. Int J Mol Sci 2021; 22:ijms22147385. [PMID: 34299026 PMCID: PMC8305213 DOI: 10.3390/ijms22147385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa and Sphingobacterium sp. are well known for their ability to decontaminate many environmental pollutants while Geobacillus sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of P. aeruginosa S3, Sphingobacterium S2 and Geobacillus EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of Sphinogobacterium strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of P. aeruginosa strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile Geobacillus strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.
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Affiliation(s)
- Sadia Mehmood Satti
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (S.M.S.); (A.A.S.)
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Shamasabad, Muree Road, Rawalpindi 46300, Pakistan
| | - Edgar Castro-Aguirre
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- Kraft Heinz Company, Glenview, IL 60025-4312, USA
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (S.M.S.); (A.A.S.)
| | - Terence L. Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-1223, USA
- Correspondence: (T.L.M.); (R.A.)
| | - Rafael Auras
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- Correspondence: (T.L.M.); (R.A.)
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15
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Hahn MW, Huemer A, Pitt A, Hoetzinger M. Opening a next-generation black box: Ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit. Mol Ecol Resour 2021; 21:2471-2485. [PMID: 34101998 DOI: 10.1111/1755-0998.13444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolving protein-encoding gene priB was used to reveal ecological patterns hidden within a single operational taxonomic unit (OTU) defined by >99% 16S rRNA sequence similarity. The studied subcluster PnecC of the genus Polynucleobacter represents a ubiquitous group of abundant freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. In addition to the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. An unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca2+ -rich and Ca2+ -poor habitats. This compositional pattern strongly resembled the vicariance of plant species on silicate and limestone soils. The new cultivation-independent approach presented opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.
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Affiliation(s)
- Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Andrea Huemer
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Matthias Hoetzinger
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
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16
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Jurburg SD, Keil P, Singh BK, Chase JM. All together now: Limitations and recommendations for the simultaneous analysis of all eukaryotic soil sequences. Mol Ecol Resour 2021; 21:1759-1771. [PMID: 33943001 DOI: 10.1111/1755-0998.13401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/31/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023]
Abstract
The soil environment contains a large, but historically underexplored, reservoir of biodiversity. Sequencing prokaryotic marker genes has become commonplace for the discovery and characterization of soil bacteria and archaea. Increasingly, this approach is also applied to eukaryotic marker genes to characterize the diversity and distribution of soil eukaryotes. However, understanding the properties and limitations of eukaryotic marker sequences is essential for correctly analysing, interpreting, and synthesizing the resulting data. Here, we illustrate several biases from sequencing data that affect measurements of biodiversity that arise from variation in morphology, taxonomy and phylogeny between organisms, as well as from sampling designs. We recommend analytical approaches to overcome these limitations, and outline how the benchmarking and standardization of sequencing protocols may improve the comparability of the data.
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Affiliation(s)
- Stephanie D Jurburg
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Petr Keil
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Computer Science, Martin Luther University, Halle-Wittenberg, Halle, Germany.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha-Suchdol, Czech Republic
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, and Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Computer Science, Martin Luther University, Halle-Wittenberg, Halle, Germany
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17
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Morimoto Y, Lu YJ, Zuo H, Aibibula Z, Tohya M, Kirikae T, Hiramatsu K, Daida H, Baba T. Pseudomonas allokribbensis sp. nov. and Pseudomonas gozinkensis sp. nov., Two New Species Isolated from a Volcanic Island, Izu Oshima, Japan. Curr Microbiol 2021; 78:1670-1677. [PMID: 33660045 DOI: 10.1007/s00284-021-02409-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/10/2021] [Indexed: 12/22/2022]
Abstract
The genomes of two Pseudomonas strains, IzPS23T and IzPS32dT isolated from soil samples of Izu Oshima were compared to Pseudomonas type strains. Whole-genome sequence analysis revealed both belong to the Pseudomonas fluorescens lineage. The average nucleotide identity values of the whole-genome sequences of IzPS23T and IzPS32dT compared with other type strains showed high correlations with Pseudomonas kribbensis (93.1%) and Pseudomonas glycinae (93.5%), respectively. Genome-to-genome distances between the whole-genome sequences of IzPS23T and IzPS32dT showed correlations with Pseudomonas kribbensis (51.0%) and Pseudomonas glycinae (53.2%), respectively. Genotypic and phenotypic analysis indicated the two strains were novel species, and were named Pseudomonas allokribbensis (IzPS23T = CECT 9961T, = LMG 31525T) and Pseudomonas gozinkensis (IzPS32dT = CECT 9962T, = LMG 31526T), respectively.
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Affiliation(s)
- Yuh Morimoto
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan.,Faculty of Health Science, Juntendo University, Tokyo, Japan
| | - Yu Jie Lu
- Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hui Zuo
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan.,Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Zulipiya Aibibula
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mari Tohya
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Teruo Kirikae
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Keiichi Hiramatsu
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan.,Center of Excellence for Infection Control Science, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hiroyuki Daida
- Faculty of Health Science, Juntendo University, Tokyo, Japan
| | - Tadashi Baba
- Department of Microbiology, Faculty of Medicine, Juntendo University, Tokyo, Japan. .,Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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18
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Fakhri H, Shahi A, Ovez S, Aydin S. Bioaugmentation with immobilized endophytic Penicillium restrictum to improve quorum quenching activity for biofouling control in an aerobic hollow-fiber membrane bioreactor treating antibiotic-containing wastewater. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 210:111831. [PMID: 33388591 DOI: 10.1016/j.ecoenv.2020.111831] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
The effects of bioaugmentation with immobilized Penicillium restrictum on the removal efficiency of sulfamethoxazole (SMX), erythromycin (ERY) and tetracycline (TC) antibiotics as well as membrane biofouling was studied using hollow-fiber membrane bioreactor (HF-MBR). Bioaugmentation with P. restrictum led to a significant change in the antibiotic removal efficiency and relative abundance of aerobic microbial community, most probably as a result of its quorum quenching activity. Furthermore, in addition to its role in the increase of SMX and ERY removal efficiencies and the decrease of their sorption on solid phase, bioaugmentation significantly reduced the transmembrane pressure which in turn reduced membrane clogging. The most abundant phyla in sludge and biofilm samples in the presence of P. restrictum were observed to be Proteobacteria, Bacteroidetes and Firmicutes. Differences in bacterial compositions and their specificity in biodegradation of antibiotics in different reactors showed that bacteria were specifically selected under the pressure of antibiotics and growing fungus.
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Affiliation(s)
- Hadi Fakhri
- Department of Environmental Engineering, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Aiyoub Shahi
- Institute of Environment, University of Tabriz, Tabriz 5166616471, Iran
| | - Suleyman Ovez
- Department of Environmental Engineering, Istanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Sevcan Aydin
- Department of Genetics and Bioengineering, Nişantaşı University, Maslak, Istanbul 34469, Turkey.
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19
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Okazaki Y, Fujinaga S, Salcher MM, Callieri C, Tanaka A, Kohzu A, Oyagi H, Tamaki H, Nakano SI. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. MICROBIOME 2021; 9:24. [PMID: 33482922 PMCID: PMC7825169 DOI: 10.1186/s40168-020-00974-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/07/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Freshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe. RESULTS Our single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7-101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion. CONCLUSIONS Our novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future. Video abstract.
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Affiliation(s)
- Yusuke Okazaki
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan.
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan.
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Shohei Fujinaga
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 37005, České Budějovice, Czech Republic
- Limnological Station, Institute of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Zurich, Switzerland
| | - Cristiana Callieri
- CNR, IRSA Institute of Water Research, Largo Tonolli 50, 28922, Verbania, Italy
| | - Atsushi Tanaka
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Ayato Kohzu
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hideo Oyagi
- Faculty of Policy Studies, Nanzan University, 18 Yamazato-cho, Showa-ku, Nagoya, Aichi, 466-8673, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Shin-Ichi Nakano
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga, 520-2113, Japan
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20
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Ghielmetti G, Rosato G, Trovato A, Friedel U, Kirchgaessner C, Perroulaz C, Pendl W, Schulthess B, Bloemberg GV, Keller PM, Stephan R, Tortoli E. Mycobacterium helveticum sp. nov., a novel slowly growing mycobacterial species associated with granulomatous lesions in adult swine. Int J Syst Evol Microbiol 2020; 71. [PMID: 33355527 PMCID: PMC7968739 DOI: 10.1099/ijsem.0.004615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The occurrence of nontuberculous mycobacteria in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. Mycobacteriosis in pigs is usually associated with members of the Mycobacterium avium complex and, in particular, with ‘Mycobacterium avium subsp. hominissuis’. Here we describe a novel slow-growing mycobacterial species isolated from lymph nodes obtained from two sows housed in different Swiss farms. The animals presented chronic inappetence and mild diarrhoea. Gross pathology revealed focal caseous lymphadenopathy of the mesenteric lymph nodes. Complete genome sequencing of the two isolates from the two sows was performed. The genomes comprised 5.76 Mb and an average nucleotide identity score of 99.97 %. Whole genome sequence, mycolic acid and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the two isolates were not related to any previously described Mycobacterium species. The closest related species was Mycobacterium parmense, a slow-growing scotochromogenic mycobacterium first isolated from a cervical lymph node of a 3-year-old child. The name proposed for the new species is Mycobacterium helveticum sp. nov. and 16-83T (=DSM 109965T= LMG 2019-02457T) is the type strain.
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Affiliation(s)
- Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Giovanni Ghielmetti,
| | - Giuliana Rosato
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Ute Friedel
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Constanze Kirchgaessner
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Carmen Perroulaz
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Wolfgang Pendl
- Department for Farm Animals, Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Bettina Schulthess
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Guido V. Bloemberg
- Institute for Food Safety and Hygiene, Swiss National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Peter M. Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
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21
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Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum "Campylobacterota". PLoS One 2020; 15:e0241366. [PMID: 33301463 PMCID: PMC7728183 DOI: 10.1371/journal.pone.0241366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.
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Bergsten E, Mestivier D, Sobhani I. The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota. Microorganisms 2020; 8:microorganisms8121954. [PMID: 33317070 PMCID: PMC7764459 DOI: 10.3390/microorganisms8121954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 01/02/2023] Open
Abstract
An increasing body of evidence highlights the role of fecal microbiota in various human diseases. However, more than two-thirds of fecal bacteria cannot be cultivated by routine laboratory techniques. Thus, physicians and scientists use DNA sequencing and statistical tools to identify associations between bacterial subgroup abundances and disease. However, discrepancies between studies weaken these results. In the present study, we focus on biases that might account for these discrepancies. First, three different DNA extraction methods (G’NOME, QIAGEN, and PROMEGA) were compared with regard to their efficiency, i.e., the quality and quantity of DNA recovered from feces of 10 healthy volunteers. Then, the impact of the DNA extraction method on the bacteria identification and quantification was evaluated using our published cohort of sample subjected to both 16S rRNA sequencing and whole metagenome sequencing (WMS). WMS taxonomical assignation employed the universal marker genes profiler mOTU-v2, which is considered the gold standard. The three standard pipelines for 16S RNA analysis (MALT and MEGAN6, QIIME1, and DADA2) were applied for comparison. Taken together, our results indicate that the G’NOME-based method was optimal in terms of quantity and quality of DNA extracts. 16S rRNA sequence-based identification of abundant bacteria genera showed acceptable congruence with WMS sequencing, with the DADA2 pipeline yielding the highest congruent levels. However, for low abundance genera (<0.5% of the total abundance) two pipelines and/or validation by quantitative polymerase chain reaction (qPCR) or WMS are required. Hence, 16S rRNA sequencing for bacteria identification and quantification in clinical and translational studies should be limited to diagnostic purposes in well-characterized and abundant genera. Additional techniques are warranted for low abundant genera, such as WMS, qPCR, or the use of two bio-informatics pipelines.
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Affiliation(s)
- Emma Bergsten
- EA7375 (EC2M3 Research Team), Université Paris Est, 94010 Créteil, France; (E.B.); (D.M.)
| | - Denis Mestivier
- EA7375 (EC2M3 Research Team), Université Paris Est, 94010 Créteil, France; (E.B.); (D.M.)
- Bioinformatics Core Facility, Institut Mondor de Recherche Biomédicale, UMR 955—Institut National de la Santé et de la Recherche Médicale—UPEC, 94010 Créteil, France
| | - Iradj Sobhani
- EA7375 (EC2M3 Research Team), Université Paris Est, 94010 Créteil, France; (E.B.); (D.M.)
- Service de Gastroenterologie, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, 94010 Créteil, France
- Correspondence: ; Tel.: +33-149814358
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Khaleque HN, González C, Johnson DB, Kaksonen AH, Holmes DS, Watkin ELJ. Genome-based classification of Acidihalobacter prosperus F5 (=DSM 105917=JCM 32255) as Acidihalobacter yilgarnensis sp. nov. Int J Syst Evol Microbiol 2020; 70:6226-6234. [PMID: 33112221 PMCID: PMC8049490 DOI: 10.1099/ijsem.0.004519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022] Open
Abstract
The genus Acidihalobacter has three validated species, Acidihalobacter ferrooxydans, Acidihalobacter prosperus and Acidihalobacter aeolinanus, all of which were isolated from Vulcano island, Italy. They are obligately chemolithotrophic, aerobic, acidophilic and halophilic in nature and use either ferrous iron or reduced sulphur as electron donors. Recently, a novel strain was isolated from an acidic, saline drain in the Yilgarn region of Western Australia. Strain F5T has an absolute requirement for sodium chloride (>5 mM) and is osmophilic, growing in elevated concentrations (>1 M) of magnesium sulphate. A defining feature of its physiology is its ability to catalyse the oxidative dissolution of the most abundant copper mineral, chalcopyrite, suggesting a potential role in biomining. Originally categorized as a strain of A. prosperus, 16S rRNA gene phylogeny and multiprotein phylogenies derived from clusters of orthologous proteins (COGS) of ribosomal protein families and universal protein families unambiguously demonstrate that strain F5T forms a well-supported separate branch as a sister clade to A. prosperus and is clearly distinguishable from A. ferrooxydans DSM 14175T and A. aeolinanus DSM14174T. Results of comparisons between strain F5T and the other Acidihalobacter species, using genome-based average nucleotide identity, average amino acid identity, correlation indices of tetra-nucleotide signatures (Tetra) and genome-to-genome distance (digital DNA-DNA hybridization), support the contention that strain F5T represents a novel species of the genus Acidihalobacter. It is proposed that strain F5T should be formally reclassified as Acidihalobacter yilgarnenesis F5T (=DSM 105917T=JCM 32255T).
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Affiliation(s)
- Himel Nahreen Khaleque
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia
- CSIRO Land and Water, Floreat, Australia
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - D. Barrie Johnson
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
- Faculty of Health and Life Sciences, Coventry University, Coventry, CV1 5RW, UK
| | | | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia y Vida, Santiago, Chile
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Universidad San Sebastian, Santiago, Chile
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24
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Rodriguez-R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ Microbiol 2020; 22:3394-3412. [PMID: 32495495 DOI: 10.1111/1462-2920.15112] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/26/2020] [Accepted: 05/31/2020] [Indexed: 01/22/2023]
Abstract
Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.
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Affiliation(s)
- Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Chengwei Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
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25
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Ellegaard KM, Suenami S, Miyazaki R, Engel P. Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species. Curr Biol 2020. [PMID: 32531278 DOI: 10.1101/2020.01.23.916296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities.
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Affiliation(s)
- Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Shota Suenami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 305-8566 Tsukuba, Japan
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 305-8566 Tsukuba, Japan; Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, 169-8555 Tokyo, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
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26
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Ellegaard KM, Suenami S, Miyazaki R, Engel P. Vast Differences in Strain-Level Diversity in the Gut Microbiota of Two Closely Related Honey Bee Species. Curr Biol 2020; 30:2520-2531.e7. [PMID: 32531278 PMCID: PMC7342003 DOI: 10.1016/j.cub.2020.04.070] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 01/31/2023]
Abstract
Most bacterial species encompass strains with vastly different gene content. Strain diversity in microbial communities is therefore considered to be of functional importance. Yet little is known about the extent to which related microbial communities differ in diversity at this level and which underlying mechanisms may constrain and maintain strain-level diversity. Here, we used shotgun metagenomics to characterize and compare the gut microbiota of two honey bee species, Apis mellifera and Apis cerana, which diverged about 6 mya. Although the host species are colonized largely by the same bacterial 16S rRNA phylotypes, we find that their communities are host specific when analyzed with genomic resolution. Moreover, despite their similar ecology, A. mellifera displayed a much higher diversity of strains and functional gene content in the microbiota compared to A. cerana, both per colony and per individual bee. In particular, the gene repertoire for polysaccharide degradation was massively expanded in the microbiota of A. mellifera relative to A. cerana. Bee management practices, divergent ecological adaptation, or habitat size may have contributed to the observed differences in microbiota genomic diversity of these key pollinator species. Our results illustrate that the gut microbiota of closely related animal hosts can differ vastly in genomic diversity while displaying similar levels of diversity based on the 16S rRNA gene. Such differences are likely to have consequences for gut microbiota functioning and host-symbiont interactions, highlighting the need for metagenomic studies to understand the ecology and evolution of microbial communities. Metagenomics reveals differences in gut microbiota diversity beyond the 16S rRNA gene Apis cerana and Apis mellifera harbor distinct species and strains in their gut Diversity is much higher in A. mellifera per individual bee and within colonies Major differences in functions are related to polysaccharide degradation
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Affiliation(s)
- Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Shota Suenami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 305-8566 Tsukuba, Japan
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 305-8566 Tsukuba, Japan; Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, 169-8555 Tokyo, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 305-8572 Tsukuba, Japan
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
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Grettenberger CL, Havig JR, Hamilton TL. Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site. BMC Microbiol 2020; 20:119. [PMID: 32423375 PMCID: PMC7236192 DOI: 10.1186/s12866-020-01768-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Ferrovum spp. are abundant in acid mine drainage sites globally where they play an important role in biogeochemical cycling. All known taxa in this genus are Fe(II) oxidizers. Thus, co-occurring members of the genus could be competitors within the same environment. However, we found multiple, co-occurring Ferrovum spp. in Cabin Branch, an acid mine drainage site in the Daniel Boone National Forest, KY. RESULTS Here we describe the distribution of Ferrovum spp. within the Cabin Branch communities and metagenome assembled genomes (MAGs) of two new Ferrovum spp. In contrast to previous studies, we recovered multiple 16S rRNA gene sequence variants suggesting the commonly used 97% cutoff may not be appropriate to differentiate Ferrovum spp. We also retrieved two nearly-complete Ferrovum spp. genomes from metagenomic data. The genomes of these taxa differ in several key ways relating to nutrient cycling, motility, and chemotaxis. CONCLUSIONS Previously reported Ferrovum genomes are also diverse with respect to these categories suggesting that the genus Ferrovum contains substantial metabolic diversity. This diversity likely explains how the members of this genus successfully co-occur in Cabin Branch and why Ferrovum spp. are abundant across geochemical gradients.
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Affiliation(s)
| | - Jeff R Havig
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, 218 Cargill Building, St. Paul, MN, 55108, USA.
- The BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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28
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Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans. Appl Environ Microbiol 2020; 86:AEM.00140-20. [PMID: 32169939 DOI: 10.1128/aem.00140-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/10/2020] [Indexed: 11/20/2022] Open
Abstract
Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCE Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.
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29
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Edge TA, Baird DJ, Bilodeau G, Gagné N, Greer C, Konkin D, Newton G, Séguin A, Beaudette L, Bilkhu S, Bush A, Chen W, Comte J, Condie J, Crevecoeur S, El-Kayssi N, Emilson EJS, Fancy DL, Kandalaft I, Khan IUH, King I, Kreutzweiser D, Lapen D, Lawrence J, Lowe C, Lung O, Martineau C, Meier M, Ogden N, Paré D, Phillips L, Porter TM, Sachs J, Staley Z, Steeves R, Venier L, Veres T, Watson C, Watson S, Macklin J. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:135906. [PMID: 31926407 DOI: 10.1016/j.scitotenv.2019.135906] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.
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Affiliation(s)
- Thomas A Edge
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Donald J Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.
| | | | - Nellie Gagné
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Charles Greer
- National Research Council Canada, Montreal, Quebec, Canada
| | - David Konkin
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Glen Newton
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | | | - Lee Beaudette
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Satpal Bilkhu
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Alexander Bush
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Wen Chen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jérôme Comte
- Environment and Climate Change Canada, Burlington, Ontario, Canada; Institut National de la Recherche Scientifique, Québec, Québec, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | | | | | - Erik J S Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Donna-Lee Fancy
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Iyad Kandalaft
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ian King
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - David Kreutzweiser
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - David Lapen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John Lawrence
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Lowe
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Oliver Lung
- Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | | | - Matthew Meier
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nicholas Ogden
- Public Health Agency of Canada, St. Hyacinthe, Quebec, Canada
| | - David Paré
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Lori Phillips
- Agriculture and Agri-Food Canada, Harrow, Ontario, Canada
| | - Teresita M Porter
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada; Biodiversity Institute of Ontario, University of Guelph, Ontario, Canada
| | - Joel Sachs
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Zachery Staley
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Royce Steeves
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Lisa Venier
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Teodor Veres
- National Research Council Canada, Ottawa, Ontario, Canada
| | - Cynthia Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Susan Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - James Macklin
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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Bradley PH, Pollard KS. phylogenize: correcting for phylogeny reveals genes associated with microbial distributions. Bioinformatics 2020; 36:1289-1290. [PMID: 31588499 PMCID: PMC7703751 DOI: 10.1093/bioinformatics/btz722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/12/2019] [Accepted: 09/25/2019] [Indexed: 11/17/2022] Open
Abstract
Summary Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME 2 and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization. Availability and implementation phylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/phylogenize. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Patrick H Bradley
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA.,Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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31
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Lewis E, Hudson JA, Cook N, Barnes JD, Haynes E. Next-generation sequencing as a screening tool for foodborne pathogens in fresh produce. J Microbiol Methods 2020; 171:105840. [PMID: 31945388 DOI: 10.1016/j.mimet.2020.105840] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 01/10/2023]
Abstract
Next generation sequencing (NGS) approaches are increasingly applied to tracing microbial contaminants entering the food chain due to NGS' untargeted nature and ability to investigate non-culturable (and/or difficult to culture) organisms while yielding genomic information about the microbiota. So far, a plethora of microbes has been shown to be associated with fresh produce, but few studies have utilised NGS to identify contamination with human pathogens. This study aims to establish the limit of detection (LoD) for Salmonella and phage MS2 (a Norovirus surrogate) contamination of fresh produce employing NGS approaches on the Illumina MiSeq: 16S amplicon-sequencing, and RNA-seq, using ScriptSeq (Illumina) and NEBNext (New England BioLabs) kits. ScriptSeq proved the most sensitive approach; delivering an LoD of 104 CFU reaction-1 (Colony Forming Units) for Salmonella and 105 PFU reaction-1 (Plaque Forming Units) for phage MS2. Use of the NEBNext kit resulted in detection of Salmonella at 106 CFU reaction-1 and phage MS2 at 107 PFU reaction-1. 16S amplicon-sequencing yielded a similar LoD of 105 CFU reaction-1 for Salmonella but could not detect MS2. The tested NGS methodologies, in combination with bioinformatics approaches applied, proved less sensitive than conventional microbial detection approaches.
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Affiliation(s)
- E Lewis
- IAFRI, Newcastle University, Newcastle upon Tyne, UK; Fera, National Agrifood Innovation Campus, Sand Hutton, York, UK.
| | | | - N Cook
- Jorvik Food Safety Services, York, UK
| | - J D Barnes
- IAFRI, Newcastle University, Newcastle upon Tyne, UK
| | - E Haynes
- Fera, National Agrifood Innovation Campus, Sand Hutton, York, UK
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32
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Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM, Cole JR, Konstantinidis KT. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res 2019; 46:W282-W288. [PMID: 29905870 PMCID: PMC6031002 DOI: 10.1093/nar/gky467] [Citation(s) in RCA: 330] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/24/2018] [Indexed: 12/05/2022] Open
Abstract
The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called ‘Clade Project’) to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.
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Affiliation(s)
- Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr. NW, Atlanta, GA 30332, USA
| | - Santosh Gunturu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - William T Harvey
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr. NW, Atlanta, GA 30332, USA
| | - Ramon Rosselló-Mora
- Grup de Microbiologia Marina, Institut Mediterrani d'Estudis Avançats (IMEDEA), Universitat de les Illes Balears (UIB) and Consejo Superior de Investigaciones Científicas (CSIC), C/Miquel Marques 21, 07190 Esporles, Illes Balears, Spain
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr. NW, Atlanta, GA 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, 310 Ferst Dr. NW, Atlanta, GA 30332, USA
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33
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Hayashi Sant’Anna F, Bach E, Porto RZ, Guella F, Hayashi Sant’Anna E, Passaglia LMP. Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy. Crit Rev Microbiol 2019; 45:182-200. [DOI: 10.1080/1040841x.2019.1569587] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fernando Hayashi Sant’Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Evelise Bach
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renan Z. Porto
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Felipe Guella
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo Hayashi Sant’Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciane M. P. Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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34
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Muscarella ME, Boot CM, Broeckling CD, Lennon JT. Resource heterogeneity structures aquatic bacterial communities. ISME JOURNAL 2019; 13:2183-2195. [PMID: 31053829 DOI: 10.1038/s41396-019-0427-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/10/2019] [Indexed: 01/20/2023]
Abstract
Microorganisms are strongly influenced by the bottom-up effects of resource supply. While many species respond to fluctuations in the concentration of resources, microbial diversity may also be affected by the heterogeneity of the resource pool, which often reflects a mixture of distinct molecules. To test this hypothesis, we examined resource-diversity relationships for bacterioplankton in a set of north temperate lakes that varied in their concentration and composition of dissolved organic matter (DOM), which is an important resource for heterotrophic bacteria. Using 16S rRNA transcript sequencing and ecosystem metabolomics, we documented strong relationships between bacterial alpha-diversity (richness and evenness) and the bulk concentration and the number of molecules in the DOM pool. Similarly, bacterial community beta-diversity was related to both DOM concentration and composition. However, in some lakes the relative abundance of resource generalists, which was inversely related to the DOM concentration, may have reduced the effect of DOM heterogeneity on community composition. Together, our results demonstrate the potential metabolic interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.
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Affiliation(s)
- Mario E Muscarella
- Department of Plant Biology, University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Claudia M Boot
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, 80523, CO, USA.,Department of Chemistry, Colorado State University, Fort Collins, 80523, CO, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, 80523, CO, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
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35
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Neumann AP, Suen G. The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential. mSphere 2018; 3:e00593-18. [PMID: 30541780 PMCID: PMC6291624 DOI: 10.1128/msphere.00593-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022] Open
Abstract
Members of the genus Fibrobacter are cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novel Fibrobacter strains against the type strains for the two formally described Fibrobacter species F. succinogenes strain S85 and F. intestinalis strain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed among Fibrobacter phylotypes. F. succinogenes genomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those of F. intestinalis strains. Moreover, genomes of F. succinogenes phylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes of F. succinogenes phylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of the Fibrobacter genomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology of Fibrobacter spp. in the herbivore gut.IMPORTANCE The herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularly Fibrobacter spp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genus Fibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolated Fibrobacter strains, to identify a robust association between carbohydrate-active enzyme gene content and the Fibrobacter phylogeny. Our results provide the strongest evidence reported to date for functional differences among Fibrobacter phylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.
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Affiliation(s)
- Anthony P Neumann
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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36
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Meziti A, Tsementzi D, Rodriguez-R LM, Hatt JK, Karayanni H, Kormas KA, Konstantinidis KT. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient. ISME JOURNAL 2018; 13:767-779. [PMID: 30397261 DOI: 10.1038/s41396-018-0307-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 09/26/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022]
Abstract
Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.
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Affiliation(s)
- Alexandra Meziti
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia
| | - Hera Karayanni
- Department of Biological Applications and Technology, University of Ioannina, 45110, Ioannina, Greece
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, 38446, Volos, Greece
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia. .,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences & Technology Building, 311 Ferst Drive, 30332, Atlanta, GA, Georgia.
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37
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Castro JC, Rodriguez-R LM, Harvey WT, Weigand MR, Hatt JK, Carter MQ, Konstantinidis KT. imGLAD: accurate detection and quantification of target organisms in metagenomes. PeerJ 2018; 6:e5882. [PMID: 30405973 PMCID: PMC6216955 DOI: 10.7717/peerj.5882] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen Escherichia coli O157:H7 and showed that its limit of detection can be comparable to that of PCR-based approaches for these samples (∼1 cell/gram).
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Affiliation(s)
- Juan C Castro
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, United States of America.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Luis M Rodriguez-R
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, United States of America.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - William T Harvey
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Michael R Weigand
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America.,Division of Bacterial Diseases, Center for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Michelle Q Carter
- Produce Safety and Microbiology, USDA-ARS Western Regional Research Center, US Department of Agriculture, Albany, CA, United States of America
| | - Konstantinos T Konstantinidis
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, United States of America.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States of America.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
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38
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Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity. mSystems 2018; 3:mSystems00039-18. [PMID: 29657970 PMCID: PMC5893860 DOI: 10.1128/msystems.00039-18] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/15/2023] Open
Abstract
Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k-mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity (Nd ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that Nd additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and limiting statistical approaches to quantify diversity. Here we described Nonpareil 3, a new bioinformatics algorithm that circumvents several of these limitations and thus can facilitate culture-independent studies in clinical or environmental settings, independent of the sequencing platform employed. In addition, we present a new metric of sequence diversity based on rarefied coverage and demonstrate its use in communities from diverse ecosystems.
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