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Bivand JM, Dyrhovden R, Sivertsen A, Tellevik MG, Patel R, Kommedal Ø. Broad-range amplification and sequencing of the rpoB gene: a novel assay for bacterial identification in clinical microbiology. J Clin Microbiol 2024:e0026624. [PMID: 38884485 DOI: 10.1128/jcm.00266-24] [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: 02/15/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The rpoB gene has been proposed as a promising phylogenetic marker for bacterial identification, providing theoretically improved species-level resolution compared to the 16S rRNA gene for a range of clinically important taxa. However, its utility in diagnostic microbiology has been limited by the lack of broad-range primers allowing for its amplification from most species with a single PCR assay. Here, we present an assay for broad-range partial amplification and Sanger sequencing of the rpoB gene. To reduce cross-reactivity and allow for rpoB amplification directly from patient samples, primers were based on the dual priming oligonucleotide principle. The resulting amplicon is ~550 base pairs in length and appropriate for species-level identification. Systematic in silico evaluation of a wide selection of taxa demonstrated improved resolution within multiple important genera, including Enterococcus, Fusobacterium, Mycobacterium, Streptococcus, and Staphylococcus species and several genera within the Enterobacteriaceae family. Broad-range rpoB amplification and Sanger sequencing of 115 bacterial isolates provided unambiguous species-level identification for 97 (84%) isolates, as compared to 57 (50%) using a clinical 16S rRNA gene assay. Several unresolved taxonomic matters disguised by the low resolution of the 16S rRNA gene were revealed using the rpoB gene. Using a collection of 33 clinical specimens harboring bacteria and assumed to contain high concentrations of human DNA, the rpoB assay identified the pathogen in 29 specimens (88%). Broad-range rpoB amplification and sequencing provides a promising tool for bacterial identification, improving discrimination between closely related species and making it amenable for use in culture-based and culture-independent diagnostic approaches.
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Affiliation(s)
- Joanna Małgorzata Bivand
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Audun Sivertsen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | | | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [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: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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3
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Parente E, Ricciardi A. A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5. Foods 2024; 13:1689. [PMID: 38890917 PMCID: PMC11171936 DOI: 10.3390/foods13111689] [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: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Amplicon-targeted metagenomics is now the standard approach for the study of the composition and dynamics of food microbial communities. Hundreds of papers on this subject have been published in scientific journals and the information is dispersed in a variety of sources, while raw sequences and their metadata are available in public repositories for some, but not all, of the published studies. A limited number of web resources and databases allow scientists to access this wealth of information but their level of annotation on studies and samples varies. Here, we report on the release of FoodMicrobionet v5, a comprehensive database of metataxonomic studies on bacterial and fungal communities of foods. The current version of the database includes 251 published studies (11 focusing on fungal microbiota, 230 on bacterial microbiota, and 10 providing data for both bacterial and fungal microbiota) and 14,035 samples with data on bacteria and 1114 samples with data on fungi. The new structure of the database is compatible with interactive apps and scripts developed for previous versions and allows scientists, R&D personnel in industries and regulators to access a wealth of information on food microbial communities.
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Affiliation(s)
- Eugenio Parente
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy;
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Padfield D, Kay S, Vos R, Quince C, Vos M. Macroevolutionary Dynamics in Micro-organisms: Generalists Give Rise to Specialists Across Biomes in the Ubiquitous Bacterial Phylum Myxococcota. Mol Biol Evol 2024; 41:msae088. [PMID: 38717941 PMCID: PMC11127111 DOI: 10.1093/molbev/msae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Prokaryotes dominate the Tree of Life, but our understanding of the macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver of prokaryote diversity. However, relatively little is known about how prokaryotes successfully transition and persist across environments, and how these processes might vary between biomes and lineages. Here, we investigate biome transitions and specialization in natural populations of a focal bacterial phylum, the Myxococcota, sampled across a range of replicated soils and freshwater and marine sediments in Cornwall (UK). By targeted deep sequencing of the protein-coding gene rpoB, we found >2,000 unique Myxococcota lineages, with the majority (77%) classified as biome specialists and with only <5% of lineages distributed across the salt barrier. Discrete character evolution models revealed that specialists in one biome rarely transitioned into specialists in another biome. Instead, evolved generalism mediated transitions between biome specialists. State-dependent diversification models found variation in speciation rates across the tree, but this variation was independent of biome association or specialization. Our findings were robust to phylogenetic uncertainty, different levels of species delineation, and different assumed amounts of unsampled diversity resulting in an incomplete phylogeny. Overall, our results are consistent with a "jack-of-all-trades" tradeoff where generalists suffer a cost in any individual environment, resulting in rapid evolution of niche specialists and shed light on how bacteria could transition between biomes.
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Affiliation(s)
- Daniel Padfield
- Environment and Sustainability Institute, Penryn Campus, Penryn TR10 9FE, UK
| | - Suzanne Kay
- Environment and Sustainability Institute, Penryn Campus, Penryn TR10 9FE, UK
| | - Rutger Vos
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich NR4 7UQ, UK
| | - Michiel Vos
- Environment and Sustainability Institute, Penryn Campus, Penryn TR10 9FE, UK
- European Centre for Environment and Human Health, Penryn Campus, Penryn TR10 9FE, UK
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Bielen A, Babić I, Vuk Surjan M, Kazazić S, Šimatović A, Lajtner J, Udiković-Kolić N, Mesić Z, Hudina S. Comparison of MALDI-TOF mass spectrometry and 16S rDNA sequencing for identification of environmental bacteria: a case study of cave mussel-associated culturable microorganisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21752-21764. [PMID: 38393570 DOI: 10.1007/s11356-024-32537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is routinely used as a rapid and cost-effective method for pathogen identification in clinical settings. In comparison, its performance in other microbiological fields, such as environmental microbiology, is still being tested, although isolates of environmental microbes are essential for in-depth in vivo studies of their biology, including biotechnological applications. We investigated the applicability of MALDI-TOF MS for the identification of bacterial isolates from a highly oligotrophic environment - Dinaric Karst caves, which likely harbor specific microorganisms. We cultured bacteria from the shell surface of the endemic mussel Congeria jalzici, one of the three known cave mussels in the world that lives in the Dinaric karst underground. The bacterial isolates were obtained by swabbing the shell surface of mussels living in microhabitats with different amounts of water: 10 air-exposed mussels, 10 submerged mussels, and 10 mussels in the hygropetric zone. A collection of 87 pure culture isolates was obtained, mostly belonging to the phylum Bacillota (72%), followed by Pseudomonadota (16%), Actinomycetota (11%), and Bacteroidota (1%). We compared the results of MALDI-TOF MS identification (Bruker databases DB-5989 and version 11, v11) with the results of 16S rDNA-based phylogenetic analysis, a standard procedure for bacterial identification. Identification to the genus level based on 16S rDNA was possible for all isolates and clearly outperformed the results from MALDI-TOF MS, although the updated MALDI-TOF MS database v11 gave better results than the DB-5989 version (85% versus 62%). However, identification to the species-level by 16S rDNA sequencing was achieved for only 17% of isolates, compared with 14% and 40% for the MALDI-TOF MS databases DB-5989 and v11 database, respectively. In conclusion, our results suggest that continued enrichment of MALDI-TOF MS libraries will result with this method soon becoming a rapid, accurate, and efficient tool for assessing the diversity of culturable bacteria from different environmental niches.
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Affiliation(s)
- Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia.
| | - Ivana Babić
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Marija Vuk Surjan
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Ana Šimatović
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Jasna Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | | | - Zrinka Mesić
- Oikon Ltd., Trg Senjskih Uskoka 1-2, 10020, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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Xu X, Nielsen LJD, Song L, Maróti G, Strube ML, Kovács ÁT. Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach. ISME COMMUNICATIONS 2023; 3:126. [PMID: 38012258 PMCID: PMC10682494 DOI: 10.1038/s43705-023-00330-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S rRNA gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification of Bacillus species. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution of Bacillus species in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for the tuf gene were not only specific for the Bacillus genus but also sufficiently discriminated species both in silico and in vitro in a mixture of 11 distinct Bacillus species. Investigating the primers using a natural soil sample, 13 dominant species were detected including Bacillus badius, Bacillus velezensis, and Bacillus mycoides as primary members, neither of which could be distinguished with 16S rRNA sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification of Bacillus species and aids the description of the ecological distribution of Bacilli in various natural environment.
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Affiliation(s)
- Xinming Xu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Lasse Johan Dyrbye Nielsen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Lijie Song
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
- BGI-Tianjin, BGI-Shenzhen, 300308, Tianjin, China
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, 6726, Szeged, Hungary
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, 2800, Lyngby, Denmark.
- Institute of Biology Leiden, Leiden University, 2333 BE, Leiden, The Netherlands.
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7
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Costa BF, Zarei-Baygi A, Md Iskander S, Smith AL. Antibiotic resistance genes fate during food waste management - Comparison between thermal treatment, hyperthermophilic composting, and anaerobic membrane bioreactor. BIORESOURCE TECHNOLOGY 2023; 388:129771. [PMID: 37739184 DOI: 10.1016/j.biortech.2023.129771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
The fate of eight different antibiotic resistance genes (ARGs) in food waste (sul1, sul2, tetO, tetW, ermF, ermB, ampC, oxa-1), intI1, and rpoB were monitored during thermal treatment (pyrolysis and incineration), hyperthermophilic composting, and anaerobic membrane bioreactor (AnMBR) treatment. ARGs in food waste ranged from 2.9 × 106 to 3.5 × 109 copies/kg with ampC being the least abundant and sul1 being the most abundant. Thermal treatment achieved removal below detection limits of all ARGs. Only two ARGs (sul1 and ampC) persisted in hyperthermophilic composting. While all genes except for ermB decreased in the AnMBR effluent relative to the food waste feed, sul1 remained at relatively high abundance. Biosolids on the contrary, accumulated tetO, ampC and sul2 in all tested operating conditions. Thermal treatment, despite limited resource recovery, provides the most effective mitigation of ARG risk in food waste.
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Affiliation(s)
- Bianca F Costa
- Astani Department of Civil and Environmental Engineering, University of Southern California, 920 Downey Way, Los Angeles, CA 90089, USA
| | - Ali Zarei-Baygi
- Astani Department of Civil and Environmental Engineering, University of Southern California, 920 Downey Way, Los Angeles, CA 90089, USA
| | - Syeed Md Iskander
- Department of Civil, Construction and Environmental Engineering, North Dakota State University, 1410 14(th) Ave N, Fargo, ND 58102, USA
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 920 Downey Way, Los Angeles, CA 90089, USA.
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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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Faure G, Saito M, Benler S, Peng I, Wolf YI, Strecker J, Altae-Tran H, Neumann E, Li D, Makarova KS, Macrae RK, Koonin EV, Zhang F. Modularity and diversity of target selectors in Tn7 transposons. Mol Cell 2023:S1097-2765(23)00367-2. [PMID: 37267947 DOI: 10.1016/j.molcel.2023.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/17/2023] [Accepted: 05/09/2023] [Indexed: 06/04/2023]
Abstract
To spread, transposons must integrate into target sites without disruption of essential genes while avoiding host defense systems. Tn7-like transposons employ multiple mechanisms for target-site selection, including protein-guided targeting and, in CRISPR-associated transposons (CASTs), RNA-guided targeting. Combining phylogenomic and structural analyses, we conducted a broad survey of target selectors, revealing diverse mechanisms used by Tn7 to recognize target sites, including previously uncharacterized target-selector proteins found in newly discovered transposable elements (TEs). We experimentally characterized a CAST I-D system and a Tn6022-like transposon that uses TnsF, which contains an inactivated tyrosine recombinase domain, to target the comM gene. Additionally, we identified a non-Tn7 transposon, Tsy, encoding a homolog of TnsF with an active tyrosine recombinase domain, which we show also inserts into comM. Our findings show that Tn7 transposons employ modular architecture and co-opt target selectors from various sources to optimize target selection and drive transposon spread.
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Affiliation(s)
- Guilhem Faure
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Makoto Saito
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sean Benler
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Iris Peng
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Jonathan Strecker
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Han Altae-Tran
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edwin Neumann
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Li
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Rhiannon K Macrae
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Ji L, Peng C, Bao X. Effect of vaginal flora on clinical outcome of frozen embryo transfer. Front Cell Infect Microbiol 2022; 12:987292. [PMID: 36619766 PMCID: PMC9815706 DOI: 10.3389/fcimb.2022.987292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Objective Vaginal microbiota imbalance is a high risk factor for premature birth, and is closely related to female pelvic inflammation and sexually transmitted diseases. The effect of vaginal microbiota on the outcome of assisted reproductive technology is still unclear. In this study, the vaginal microbial composition and the pregnancy outcome of frozen embryo transfer (FET) was investigated. Methods From October 2020 to December 2021, 275 FET cycles were selected from the center of reproductive medicine in Affiliated Hospital of Nantong University. Vaginal secretions were collected on the day of endometrium transformation, and smears were Gram stained. According to the Nugent score they were divided into three groups, including normal group, mild dysbiosis group and sever dysbiosis group. The clinical outcomes of each group were compared. Results In 275 FET cycles, the embryo implantation rate, clinical pregnancy rate and ongoing pregnancy rate in the normal group (66.9%,84.3% and 83.1%) were significantly higher than those in the mild dysbiosis group (45.5%, 57.3% and 49.3%) and in sever dysbiosis group (29.6%, 34.2% and 27%). The difference was statistically significant (P<0.01). When compared the preclinical pregnancy loss rate and the miscarriage rate, the normal group (1.3% and 1.3%) was significantly lower than those in the mild dysbiosis group (20.4% and 14.0%) and the sever dysbiosis group (25.5% and 21.1%). The difference was statistically significant (P<0.01), but there was no significant difference between the mild dysbiosis group and sever dysbiosis group (P>0.05). Conclusion Nugent score is directly related to the clinical outcome of FET. The Lactobacilli-dominant vaginal flora was a favorable factor for the good clinical outcome of FET, while asymptomatic bacterial vaginosis had a negative correlation with the outcome of FET.
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Affiliation(s)
- Li Ji
- Center for Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China,Department of Clinical Medicine, Nantong University, Nantong, Jiangsu, China
| | - Chen Peng
- Center for Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China,*Correspondence: Chen Peng,
| | - Xueyun Bao
- Center for Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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11
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Costa LVD, Miranda RVDSLD, Reis CMFD, Andrade JMD, Cruz FV, Frazão AM, Fonseca ELD, Ramos JN, Brandão MLL, Vieira VV. MALDI-TOF MS database expansion for identification of Bacillus and related genera isolated from a pharmaceutical facility. J Microbiol Methods 2022; 203:106625. [PMID: 36403787 DOI: 10.1016/j.mimet.2022.106625] [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: 10/15/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Bacillus and related genera are among the main bacterial groups isolated from pharmaceutical production areas. The identification of Bacillus species and related genera by classical methods is particularly difficult, due to similarities between closely related species. The Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is one of the most promising techniques for chemotaxonomic characterization of microorganisms, being an alternative to genotypic methods. This study aimed to identify Bacillus strains and related genera isolated from immunobiological production areas by phylogenetic analysis of housekeeping genes and expand the database associated with MALDI-TOF MS to improve their identification. In a previous study, 97 aerobic endospore-forming bacteria isolated from a pharmaceutical facility were analyzed by MALDI-TOF MS and 16S rRNA gene full-length sequencing. All strains were identified as Bacillus and related genera by the latest methodology. Among the 97 strains, 22 were unidentified and 2 strains were misidentified by MALDI-TOF MS. In the present study, these 24 strains were subjected to 16S rRNA gene phylogenetic analysis. Strains not identified at species level by this methodology were submitted to rpoB gene phylogenetic analysis. After identifying the strains, 19 of the 24 strains were incubated for 24, 48, and 72 h on Tryptic Soy Agar and Sheep Blood Agar and subjected to analysis by MALDI-TOF MS. A SuperSpectrum for each strain was created and entered into the equipment database. Finally, the 24 strains were again submitted to proteomic analysis by MALDI-TOF MS, and, at this time, all were correctly identified. The genotypic identification of in-house isolated strains and the introduction of these spectra in MALDI-TOF MS, in order to obtain a customized database, proved to be an extremely effective tool in the identification of Bacillus and related genera from pharmaceutical industry origin.
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Affiliation(s)
- Luciana Veloso da Costa
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil.
| | | | | | - Joyce Modesto de Andrade
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Fernanda Ventura Cruz
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Adriana Marques Frazão
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Erica Louro da Fonseca
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Juliana Nunes Ramos
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz (IOC), Interdisciplinary Medical Research Laboratory, Brazil
| | - Marcelo Luiz Lima Brandão
- Fundação Oswaldo Cruz, Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Microbiological Control Laboratory, Brazil
| | - Verônica Viana Vieira
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz (IOC), Interdisciplinary Medical Research Laboratory, Brazil
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12
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Liu Y, Štefanič P, Miao Y, Xue Y, Xun W, Zhang N, Shen Q, Zhang R, Xu Z, Mandic-Mulec I. Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study. AMB Express 2022; 12:133. [DOI: 10.1186/s13568-022-01477-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractBacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species. The amplification efficiency for Bacillus species diversity could be greatly improved by primer design. Therefore, we designed a novel primer pair gyrA3 that can detect at least 92 Bacillus species and related species. For B. amyloliquefaciens, B. pumilus, and B. megaterium, we observed that the high variability of the gyrA gene allows for more detailed clustering at the subspecies level that cannot be achieved by the 16S rRNA gene. Since gyrA provides better phylogenetic resolution than 16S rRNA and informs on the diversity of the Bacillus community, we propose that the gyrA gene may have broad application prospects in the study of Bacillus ecology.
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13
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Khosravi AD, Hashemzadeh M, Rokhfirooz P. Molecular identification of nontuberculous mycobacteria using the rpoB, argH and cya genes analysis. AMB Express 2022; 12:121. [PMID: 36121509 PMCID: PMC9483868 DOI: 10.1186/s13568-022-01463-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Nontuberculous mycobacterial (NTM) infections are growing worldwide especially in immunocompromised individuals. Since treatment of NTM infections is species-specific, the precise identification of NTM to species level is critical for an optimal treatment. This study was aimed to identify different NTM species by sequencing the rpoB gene and evaluating the effectiveness of argH and cya gene markers. In total 64 clinical isolates suspected to NTM were collected. The identification of the isolates was done by standard conventional methods and PCR-based rpoB gene and sequence analysis. PCR sequencing of argH and cya genes was performed to evaluate the efficacy of these genes in identifying and differentiating different species and subspecies of NTM. Among 64 isolates tested, 51 (79.68%) were detected by conventional tests as NTM. The results of rpoB sequence analysis revealed that the 56 clinical isolates were identified in 10 species of NTM and 8 remaining isolates which showed ambiguous results by rpoB sequencing, application of argH and cya sequencing could detect these isolates. Furthermore, by using cya gene sequencing, M. abscessus subspecies were properly differentiated. Although the rpoB sequencing as a standard method, is beneficial for detecting various species of NTM, however, based on our findings, argH and cya gene markers have a superb ability to discriminate closely related species. Further investigations are required to verify our outcomes.
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Affiliation(s)
- Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Iranian Group On Microbial Drug Resistance, Tehran, Iran
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parisa Rokhfirooz
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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14
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Soto-Dávila M, Chakraborty S, Santander J. Relative expression and validation of Aeromonas salmonicida subsp. salmonicida reference genes during ex vivo and in vivo fish infection. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105320. [PMID: 35753622 DOI: 10.1016/j.meegid.2022.105320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The genus Aeromonas is found worldwide in freshwater and marine environments and has been implicated in the etiology of human and animal diseases. In fish, among Aeromonas species, A. salmonicida causes massive mortality and great economic losses in marine and continental aquaculture species. Currently, several aspects of the clinical signs and pathogenesis of this Gram-negative bacterium have been described; however, determination of an appropriate reference gene is essential to normalize cellular mRNA data remain unknown. Here we evaluate the stability of seven candidate reference genes to be used for data normalization during ex vivo and in vivo experiments conducted in Atlantic cod, Atlantic salmon, and lumpfish. To assess this, raw Ct values obtained were evaluated by using geNorm, NormFinder, BestKeeper, Delta Ct comparison, and the comprehensive ranking, through the bioinformatic open-access portal RefFinder. We determined that fabD and era were most suitable reference genes in Atlantic cod primary macrophages, hfq and era in Atlantic salmon primary macrophages, rpoB and fabD in lumpfish head kidney samples, and hfq and era in lumpfish spleen. Our study demonstrates that use of multiple reference genes and its validation before measurements helps to minimize variability arising in qPCR studies that evaluate A. salmonicida gene expression in fish tissues. Overall, this study provided with an expanded list of reliable reference genes for A. salmonicida gene expression using qPCR during fish infection studies.
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Affiliation(s)
- Manuel Soto-Dávila
- Marine Microbial Pathogenesis and Vaccinology Lab, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada; Department of Biology, Faculty of Science, University of Waterloo, Waterloo, ON, Canada
| | - Setu Chakraborty
- Marine Microbial Pathogenesis and Vaccinology Lab, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Javier Santander
- Marine Microbial Pathogenesis and Vaccinology Lab, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada.
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15
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Liu J, Clarke JA, McCann S, Hillier NK, Tahlan K. Analysis of Streptomyces Volatilomes Using Global Molecular Networking Reveals the Presence of Metabolites with Diverse Biological Activities. Microbiol Spectr 2022; 10:e0055222. [PMID: 35900081 PMCID: PMC9431705 DOI: 10.1128/spectrum.00552-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/09/2022] [Indexed: 12/20/2022] Open
Abstract
Streptomyces species produce a wide variety of specialized metabolites, some of which are used for communication or competition for resources in their natural environments. In addition, many natural products used in medicine and industry are derived from Streptomyces, and there has been interest in their capacity to produce volatile organic compounds (VOCs) for different industrial and agricultural applications. Recently, a machine-learning workflow called MSHub/GNPS was developed, which enables auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data, molecular networking, and library search capabilities, but it has not been applied to Streptomyces volatilomes. In this study, 131 Streptomyces isolates from the island of Newfoundland were phylogenetically typed, and 37 were selected based on their phylogeny and growth characteristics for VOC analysis using both a user-guided (conventional) and an MSHub/GNPS-based approach. More VOCs were annotated by MSHub/GNPS than by the conventional method. The number of unknown VOCs detected by the two methods was higher than those annotated, suggesting that many novel compounds remain to be identified. The molecular network generated by GNPS can be used to guide the annotation of such unknown VOCs in future studies. However, the number of overlapping VOCs annotated by the two methods is relatively small, suggesting that a combination of analysis methods might be required for robust volatilome analysis. More than half of the VOCs annotated with high confidence by the two approaches are plant-associated, many with reported bioactivities such as insect behavior modulation. Details regarding the properties and reported functions of such VOCs are described. IMPORTANCE This study represents the first detailed analysis of Streptomyces volatilomes using MSHub/GNPS, which in combination with a routinely used conventional method led to many annotations. More VOCs could be annotated using MSHub/GNPS as compared to the conventional method, many of which have known antimicrobial, anticancer, and insect behavior-modulating activities. The identification of numerous plant-associated VOCs by both approaches in the current study suggests that their production could be a more widespread phenomenon by members of the genus, highlighting opportunities for their large-scale production using Streptomyces. Plant-associated VOCs with antimicrobial activities, such as 1-octen-3-ol, octanol, and phenylethyl alcohol, have potential applications as fumigants. Furthermore, many of the annotated VOCs are reported to influence insect behavior, alluding to a possible explanation for their production based on the functions of other recently described Streptomyces VOCs in dispersal and nutrient acquisition.
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Affiliation(s)
- Jingyu Liu
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Jody-Ann Clarke
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Sean McCann
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - N. Kirk Hillier
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
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16
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Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. MICROBIOME 2022; 10:104. [PMID: 35799218 PMCID: PMC9264627 DOI: 10.1186/s40168-022-01295-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/23/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82]. RESULTS At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%). CONCLUSIONS Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.
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Affiliation(s)
- Hayley B. Hassler
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Brett Probert
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Carson Moore
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | - Elizabeth Lawson
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
| | | | - Brook T. Russell
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634 USA
| | - Vincent P. Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634 USA
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17
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Buresova‐Faitova A, Kopecky J, Sagova‐Mareckova M, Alonso L, Vautrin F, Moënne‐Loccoz Y, Rodriguez‐Nava V. Comparison of
Actinobacteria
communities from human‐impacted and pristine karst caves. Microbiologyopen 2022; 11:e1276. [PMID: 35478281 PMCID: PMC8988830 DOI: 10.1002/mbo3.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 11/07/2022] Open
Abstract
Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization‐related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, and Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas‐1, Passage, Apse, and Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65‐related taxonomic database was constructed for the identification of Actinobacteria to the species level by Illumina‐MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% operational taxonomic units cutoff) versus the 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species‐level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.
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Affiliation(s)
- Andrea Buresova‐Faitova
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
- Department of Ecology, Faculty of ScienceCharles University in PraguePrague 2PragueCzech Republic
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Jan Kopecky
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Marketa Sagova‐Mareckova
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Lise Alonso
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Florian Vautrin
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Yvan Moënne‐Loccoz
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Veronica Rodriguez‐Nava
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
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Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity. mBio 2022; 13:e0317521. [PMID: 35073752 PMCID: PMC8787475 DOI: 10.1128/mbio.03175-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Methylobacterium is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. In two temperate forests, we investigated how phylogenetic diversity within Methylobacterium is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we uncovered a considerable diversity of Methylobacterium in the phyllosphere. We cultured different subsets of Methylobacterium lineages depending upon the temperature of isolation and growth (20°C or 30°C), suggesting long-term adaptation to temperature. To a lesser extent than temperature adaptation, Methylobacterium diversity was also structured across large (>100 km; between forests) and small (<1.2 km; within forests) geographical scales, among host tree species, and was dynamic over seasons. By measuring the growth of 79 isolates during different temperature treatments, we observed contrasting growth performances, with strong lineage- and season-dependent variations in growth strategies. Finally, we documented a progressive replacement of lineages with a high-yield growth strategy typical of cooperative, structured communities in favor of those characterized by rapid growth, resulting in convergence and homogenization of community structure at the end of the growing season. Together, our results show how Methylobacterium is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This work paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus. IMPORTANCE Methylobacterium is a bacterial group tied to plants. Despite the ubiquity of methylobacteria and the importance to their hosts, little is known about the processes driving Methylobacterium community dynamics. By combining traditional culture-dependent and -independent (metabarcoding) approaches, we monitored Methylobacterium diversity in two temperate forests over a growing season. On the surface of tree leaves, we discovered remarkably diverse and dynamic Methylobacterium communities over short temporal (from June to October) and spatial (within 1.2 km) scales. Because we cultured different subsets of Methylobacterium diversity depending on the temperature of incubation, we suspected that these dynamics partly reflected climatic adaptation. By culturing strains under laboratory conditions mimicking seasonal variations, we found that diversity and environmental variations were indeed good predictors of Methylobacterium growth performances. Our findings suggest that Methylobacterium community dynamics at the surface of tree leaves results from the succession of strains with contrasting growth strategies in response to environmental variations.
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Applicability of rpoB Gene for PCR-RFLP based Discrimination of Bifidobacterial Species Isolated from Human and Animal Sources. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bifidobacteria are widely used as probiotics for their application in the development of functional food and prophylactic therapy. This has necessitated the development of a molecular approach for the genera to be widely identified up to species and subspecies level. In the current study, PCR-RFLP of the partial RNA polymerase β-subunit (rpoB) gene fragment was evaluated for differential identification of Bifidobacterium species. The rpoB gene partial sequences of 575 bp were amplified from 93 previously identified isolates collected from various sources of human and animal origin along with 12 standard reference strains. The PCR amplified products were digested with three restriction endonucleases HhaI, HinfI and BanI separately. Dendrograms constructed from the patterns of HhaI, were found to be more discriminatory and successfully differentiated all the twelve species and also at sub-species level in between B. longum subsp. longum and B. longum subsp. infantis. However, B. adolescentis and B. pseudocatenulatum group clusters were not separated and represented by one group. The groups were further discriminated by HinfI restriction digestion. A separate combination thereof may be used for inferring the classification of bifidobacterial species targeted on rpoB PCR-RFLP analysis. To our knowledge, this work is the first report based on use of rpoB PCR-RFLP for discrimination of the isolates of genus Bifidobacterium and also provides insights into specific advantages of this method over hsp60 PCR-RFLP in differentiating B. longum subsp. longum and B. longum subsp. infantis.
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20
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Bajagai YS, Trotter M, Williams TM, Costa DFA, Whitton MM, Ren X, Wilson CS, Stanley D. The role of microbiota in animal health and productivity: misinterpretations and limitations. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Abellan-Schneyder I, Schusser AJ, Neuhaus K. ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples. BMC Microbiol 2021; 21:349. [PMID: 34922460 PMCID: PMC8684222 DOI: 10.1186/s12866-021-02391-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND One limiting factor of short amplicon 16S rRNA gene sequencing approaches is the use of low DNA amounts in the amplicon generation step. Especially for low-biomass samples, insufficient or even commonly undetectable DNA amounts can limit or prohibit further analysis in standard protocols. RESULTS Using a newly established protocol, very low DNA input amounts were found sufficient for reliable detection of bacteria using 16S rRNA gene sequencing compared to standard protocols. The improved protocol includes an optimized amplification strategy by using a digital droplet PCR. We demonstrate how PCR products are generated even when using very low concentrated DNA, unable to be detected by using a Qubit. Importantly, the use of different 16S rRNA gene primers had a greater effect on the resulting taxonomical profiles compared to using high or very low initial DNA amounts. CONCLUSION Our improved protocol takes advantage of ddPCR and allows faithful amplification of very low amounts of template. With this, samples of low bacterial biomass become comparable to those with high amounts of bacteria, since the first and most biasing steps are the same. Besides, it is imperative to state DNA concentrations and volumes used and to include negative controls indicating possible shifts in taxonomical profiles. Despite this, results produced by using different primer pairs cannot be easily compared.
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Affiliation(s)
- Isabel Abellan-Schneyder
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Andrea Janina Schusser
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.
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22
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Mousavi SA, Gao Y, Penttinen P, Frostegård Å, Paulin L, Lindström K. Using amplicon sequencing of rpoB for identification of inoculant rhizobia from peanut nodules. Lett Appl Microbiol 2021; 74:204-211. [PMID: 34753197 DOI: 10.1111/lam.13599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 12/16/2022]
Abstract
To improve the nitrogen fixation, legume crops are often inoculated with selected effective rhizobia. However, there is large variation in how well the inoculant strains compete with the indigenous microflora in soil. To assess the success of the inoculant, it is necessary to distinguish it from other, closely related strains. Methods used until now have generally been based either on fingerprinting methods or on the use of reporter genes. Nevertheless, these methods have their shortcomings, either because they do not provide sufficiently specific information on the identity of the inoculant strain, or because they use genetically modified organisms that need prior authorization to be applied in the field or other uncontained environments. Another possibility is to target a gene that is naturally present in the bacterial genomes. Here we have developed a method that is based on amplicon sequencing of the bacterial housekeeping gene rpoB, encoding the beta-subunit of the RNA polymerase, which has been proposed as an alternative to the 16S rRNA gene to study the diversity of rhizobial populations in soils. We evaluated the method under laboratory and field conditions. Peanut seeds were inoculated with various Bradyrhizobium strains. After nodule development, DNA was extracted from selected nodules and the nodulating rhizobia were analysed by amplicon sequencing of the rpoB gene. The analyses of the sequence data showed that the method reliably identified bradyrhizobial strains in nodules, at least at the species level, and could be used to assess the competitiveness of the inoculant compared to other bradyrhizobia.
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Affiliation(s)
- S A Mousavi
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland.,Division of Ecology and Evolutionary Biology, Department of Biology, University of Turku, Turku, Finland
| | - Y Gao
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland.,Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway.,International Research and Development Center, Kingenta Ecological Engineering Group Co. Ltd, Linyi, China
| | - P Penttinen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Å Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, As, Norway
| | - L Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - K Lindström
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Helsinki, Finland
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23
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Liu Y, Pei T, Yi S, Du J, Zhang X, Deng X, Yao Q, Deng MR, Zhu H. Phylogenomic Analysis Substantiates the gyrB Gene as a Powerful Molecular Marker to Efficiently Differentiate the Most Closely Related Genera Myxococcus, Corallococcus, and Pyxidicoccus. Front Microbiol 2021; 12:763359. [PMID: 34707598 PMCID: PMC8542856 DOI: 10.3389/fmicb.2021.763359] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/22/2021] [Indexed: 11/15/2022] Open
Abstract
Rapid and accurate strain identification of the most closely related genera Myxococcus, Corallococcus, and Pyxidicoccus can enhance the efficiency of the mining of novel secondary metabolites through dereplication. However, the commonly used 16S rRNA gene sequencing cannot accurately differentiate members of the three genera above, and the whole-genome sequencing is unable to rapidly and inexpensively provide species assignation toward a large number of isolates. To overcome the limitations, the gyrB gene was investigated as a candidate genetic marker for exploring the phylogenetic relationships of bacteria within the three genera and for developing the gyrB-based typing method. Here, the bacterial phylogeny and species affiliations of the three genera were determined based on the phylogenomic reconstruction and the analysis of digital DNA–DNA hybridization values among 90 genomes, further confirming nine novel taxa and assigning over one-third of genomes to defined species. The phylogenetic relationships of these strains based on the gyrB gene sequences were congruent with those based on their genome sequences, allowing the use of the gyrB gene as a molecular marker. The gyrB gene-specific primers for the PCR-amplification and sequencing of bacteria within the three genera were designed and validated for 31 isolates from our group collection. The gyrB-based taxonomic tool proved to be able to differentiate closely related isolates at the species level. Based on the newly proposed 98.6% identity threshold for the 966-bp gyrB gene and the phylogenetic inference, these isolates were assigned into two known species and eight additional putative new species. In summary, this report demonstrated that the gyrB gene is a powerful phylogenetic marker for taxonomy and phylogeny of bacteria within the closely related genera Myxococcus, Corallococcus, and Pyxidicoccus, particularly in the case of hundreds or thousands of isolates in environmental studies.
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Affiliation(s)
- Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Shuoxing Yi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Juan Du
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xianjiao Zhang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoqin Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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24
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Hua Z, Ouellette M, Makkay AM, Papke RT, Zhaxybayeva O. Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus. THE ISME JOURNAL 2021; 15:2853-2864. [PMID: 33846564 PMCID: PMC8443641 DOI: 10.1038/s41396-021-00960-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 02/01/2023]
Abstract
All environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities used DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. The preferential eDNA consumption and differential growth under various nutrient availability regimes were associated with substantial shifts in the taxonomic composition and diversity of microcosm communities. Therefore, we conjecture that in salterns the microbial community assembly is driven by the available resources, including eDNA.
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Affiliation(s)
- Zhengshuang Hua
- grid.254880.30000 0001 2179 2404Department of Biological Sciences, Dartmouth College, Hanover, NH USA ,grid.59053.3a0000000121679639Present Address: Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Matthew Ouellette
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA ,grid.38142.3c000000041936754XPresent Address: The Forsyth Institute, Cambridge, MA USA ,grid.38142.3c000000041936754XPresent Address: Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA USA
| | - Andrea M. Makkay
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA
| | - R. Thane Papke
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA
| | - Olga Zhaxybayeva
- grid.254880.30000 0001 2179 2404Department of Biological Sciences, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Department of Computer Science, Dartmouth College, Hanover, NH USA
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25
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Halimeh FB, Rafei R, Osman M, Kassem II, Diene SM, Dabboussi F, Rolain JM, Hamze M. Historical, current, and emerging tools for identification and serotyping of Shigella. Braz J Microbiol 2021; 52:2043-2055. [PMID: 34524650 PMCID: PMC8441030 DOI: 10.1007/s42770-021-00573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
The Shigella genus includes serious foodborne disease etiologic agents, with 4 species and 54 serotypes. Identification at species and serotype levels is a crucial task in microbiological laboratories. Nevertheless, the genetic similarity between Shigella spp. and Escherichia coli challenges the correct identification and serotyping of Shigella spp., with subsequent negative repercussions on surveillance, epidemiological investigations, and selection of appropriate treatments. For this purpose, multiple techniques have been developed historically ranging from phenotype-based methods and single or multilocus molecular techniques to whole-genome sequencing (WGS). To facilitate the selection of the most relevant method, we herein provide a global overview of historical and emerging identification and serotyping techniques with a particular focus on the WGS-based approaches. This review highlights the excellent discriminatory power of WGS to more accurately elucidate the epidemiology of Shigella spp., disclose novel promising genomic targets for surveillance methods, and validate previous well-established methods.
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Affiliation(s)
- Fatima Bachir Halimeh
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14850, USA
| | - Issmat I Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223-1797, USA
| | - Seydina M Diene
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- Aix-Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Médecine Et de Pharmacie, 19-21 boulevard Jean Moulin, 13385, Marseille CEDEX 05, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
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26
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Wang X, Feng H, Wang Y, Wang M, Xie X, Chang H, Wang L, Qu J, Sun K, He W, Wang C, Dai C, Chu Z, Tian C, Yu N, Zhang X, Liu H, Wang E. Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia-legume symbiosis. MOLECULAR PLANT 2021; 14:503-516. [PMID: 33309942 DOI: 10.1016/j.molp.2020.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/02/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. Plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula by performing quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in the rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that AM symbiosis affects Rhizobiales hubs among plant microbiota and benefits the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.
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Affiliation(s)
- Xiaolin Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Huan Feng
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mingxing Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xingguang Xie
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Huizhong Chang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Like Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jicheng Qu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wei He
- Shanghai Hanyubio Co., Ltd, Shanghai 201201, China
| | - Chunyan Wang
- College of Forestry, Northwest A&F University, Yangling 712100, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, China
| | - Changfu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Nan Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xuebin Zhang
- Center for Multi-Omics Research, Collaborative Innovation Center of Crop Stress Biology, Henan Province, Kaifeng 475001, China; Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475001, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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27
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Sevillano M, Dai Z, Calus S, Bautista-de Los Santos QM, Eren AM, van der Wielen PWJJ, Ijaz UZ, Pinto AJ. Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141451. [PMID: 32836121 DOI: 10.1016/j.scitotenv.2020.141451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/10/2020] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
Antimicrobial resistance (AMR) in drinking water has received less attention than its counterparts in the urban water cycle. While culture-based techniques or gene-centric PCR have been used to probe the impact of treatment approaches (e.g., disinfection) on AMR in drinking water, to our knowledge there is no systematic comparison of AMR trait distribution and prevalence between disinfected and disinfectant residual-free drinking water systems. We used metagenomics to assess the associations between disinfectant residuals and AMR prevalence and its host association in full-scale drinking water distribution systems (DWDSs) with and without disinfectant residuals. While the differences in AMR profiles between DWDSs were associated with the presence or absence of disinfectant, they were also associated with overall water chemistry and more importantly with microbial community structure. AMR genes and mechanisms differentially abundant in disinfected systems were primarily associated with nontuberculous mycobacteria (NTM). Finally, evaluation of metagenome assembled genomes (MAGs) also suggests that NTM possessing AMR genes conferring intrinsic resistance to key antibiotics were prevalent in disinfected systems, whereas such NTM genomes were not detected in disinfectant residual free DWDSs. Altogether, our findings provide insights into the drinking water resistome and its association with potential opportunistic pathogens, particularly in systems with disinfectant residual.
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Affiliation(s)
- Maria Sevillano
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Zihan Dai
- Infrastructure and Environmental Research Division, School of Engineering, University of Glasgow, G12 8LT Glasgow, UK
| | - Szymon Calus
- Infrastructure and Environmental Research Division, School of Engineering, University of Glasgow, G12 8LT Glasgow, UK
| | | | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA; Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Paul W J J van der Wielen
- KWR Watercycle Research Institute, Nieuwegein, Netherlands; Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Umer Z Ijaz
- Infrastructure and Environmental Research Division, School of Engineering, University of Glasgow, G12 8LT Glasgow, UK
| | - Ameet J Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA.
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28
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Zarei-Baygi A, Wang P, Harb M, Stadler LB, Smith AL. Membrane Fouling Inversely Impacts Intracellular and Extracellular Antibiotic Resistance Gene Abundances in the Effluent of an Anaerobic Membrane Bioreactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:12742-12751. [PMID: 32875793 DOI: 10.1021/acs.est.0c04787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anaerobic membrane bioreactors (AnMBRs) can significantly reduce the release of antibiotic resistance elements to the environment. The purpose of this study was to elucidate the role of membrane fouling layers (biofilms) in mitigating the release of intracellular and extracellular antibiotic resistance genes (iARGs and eARGs) from an AnMBR. The AnMBR was equipped with three membrane modules, each exhibiting a different level of fouling. Results showed that the absolute abundance of ARGs decreased gradually in the suspended biomass during operation of the AnMBR. Normalized abundances of targeted ARGs and intI1 were found to be significantly higher in the fouling layers compared to the suspended biomass, implying adsorption or an increased potential for horizontal gene transfer of ARGs in the biofilm. Effluent ARG data revealed that the highly fouled (HF) membrane significantly reduced the absolute abundance of eARGs. However, the HF membrane effluent concomitantly had the highest absolute abundance of iARGs. Nevertheless, total ARG abundance (sum of iARG and eARG) in the effluent of the AnMBR was not impacted by the extent of fouling. These results suggest a need for a combination of different treatment technologies to effectively prevent antibiotic resistance proliferation associated with these two ARG fractions.
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Affiliation(s)
- Ali Zarei-Baygi
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 S Vermont Avenue, Los Angeles, California 90089, United States
| | - Phillip Wang
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 S Vermont Avenue, Los Angeles, California 90089, United States
| | - Moustapha Harb
- Department of Civil and Environmental Engineering, Lebanese American University, 309 Bassil Building, Byblos 1102, Lebanon
| | - Lauren B Stadler
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Adam L Smith
- Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 S Vermont Avenue, Los Angeles, California 90089, United States
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29
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Rettenmaier R, Lo YK, Schmidt L, Munk B, Lagkouvardos I, Neuhaus K, Schwarz W, Liebl W, Zverlov V. A Novel Primer Mixture for GH48 Genes: Quantification and Identification of Truly Cellulolytic Bacteria in Biogas Fermenters. Microorganisms 2020; 8:E1297. [PMID: 32854333 PMCID: PMC7565076 DOI: 10.3390/microorganisms8091297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 12/22/2022] Open
Abstract
Genomic studies revealed the glycoside hydrolases of family 48 (GH48) as a powerful marker for the identification of truly cellulolytic bacteria. Here we report an improved method for detecting cellulolytic bacteria in lab-scale biogas fermenters by using GH48 genes as a molecular marker in DNA and RNA samples. We developed a mixture of primers for the specific amplification of a GH48 gene region in a broad range of bacteria. Additionally, we built a manually curated reference database containing GH48 gene sequences directly linked to the corresponding taxonomic information. Phylogenetic correlation analysis of GH48 to 16S rRNA gene sequences revealed that GH48 gene sequences with 94% identity belong with high confidence to the same genus. Applying this analysis, GH48 amplicon reads revealed that at mesophilic fermenter conditions, 50-99% of the OTUs appear to belong to novel taxa. In contrast, at thermophilic conditions, GH48 gene sequences from the genus Hungateiclostridium dominated with 60-91% relative abundance. The novel primer combinations enabled detection and relative quantification of a wide spectrum of GH48 genes in cellulolytic microbial communities. Deep phylogenetic correlation analysis and a simplified taxonomic identification with the novel database facilitate identification of cellulolytic organisms, including the detection of novel taxa in biogas fermenters.
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Affiliation(s)
- Regina Rettenmaier
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Yat Kei Lo
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Larissa Schmidt
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Bernhard Munk
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Lange Point 6, 85354 Freising, Germany;
| | - Ilias Lagkouvardos
- ZIEL—Core Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (K.N.)
| | - Klaus Neuhaus
- ZIEL—Core Facility Microbiome, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (I.L.); (K.N.)
| | - Wolfgang Schwarz
- Aspratis GmbH. Munich, Germany, Hübnerstr. 11, 80637 Munich, Germany;
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany; (R.R.); (Y.K.L.); (L.S.); (W.L.)
- Institute of Molecular Genetics of National Research Centre (Kurchatov Institute), Kurchatov Sq. 2, 123182 Moscow, Russia
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Halimeh FB, Rafei R, Diene S, Mikhael M, Mallat H, Achkar M, Dabboussi F, Hamze M, Rolain JM. Challenges in identification of enteroinvasive Escherichia coli and Shigella spp. in Lebanon. Acta Microbiol Immunol Hung 2020; 67:100-106. [PMID: 32223306 DOI: 10.1556/030.2020.01102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 12/23/2019] [Indexed: 02/01/2023]
Abstract
This study aimed to evaluate the routine identification tools available in Lebanon for differentiation of Escherichia coli and Shigella spp. The identification of 43 isolates defined as Shigella spp. by Api 20E was accessed using MALDI-TOF, serological testing, duplex PCR targeting ipaH (present in Shigella spp. and enteroinvasive E. coli "EIEC") and lacY (found in E. coli including EIEC but not Shigella spp.) as well as gyrB gene sequencing. Antibiotic susceptibility was investigated as well as Shiga-toxin production. All isolates were identified as E. coli by MALDI-TOF while the PCR showed a disparate group of 26 EIEC, 11 Shigella spp., 5 E. coli and 1 inactive E. coli. However, the sequencing of gyrB gene, which was recently described as a suitable marker for distinguishing E. coli and Shigella spp., identified all isolates as E. coli. Antibiotic resistance was noticeable against ß-lactams, rifampicin, trimethoprim-sulfamethoxazole, gentamicin, and ciprofloxacin. The most common variants of beta-lactamase genes were blaTEM-1, blaCTX-M-15, and blaCTX-M-3. A great discordance between the used methods in identification was revealed herein. An accurate identification technique able to distinguish E. coli from Shigella spp. in routine laboratories is a pressing need in order to select the appropriate treatment and assess the epidemiology of these bacteria.
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Affiliation(s)
- Fatima Bachir Halimeh
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
- 2Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Rayane Rafei
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Seydina Diene
- 2Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Mary Mikhael
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Hassan Mallat
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marcel Achkar
- 3Laboratory of Clinical Biology, NINI Hospital, Tripoli, Lebanon
| | - Fouad Dabboussi
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- 1Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Science and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Marc Rolain
- 2Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
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Willis JR, Gabaldón T. The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems. Microorganisms 2020; 8:microorganisms8020308. [PMID: 32102216 PMCID: PMC7074908 DOI: 10.3390/microorganisms8020308] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023] Open
Abstract
Abstract: The human oral cavity is home to an abundant and diverse microbial community (i.e., the oral microbiome), whose composition and roles in health and disease have been the focus of intense research in recent years. Thanks to developments in sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore the diversity and roles of oral microbes, even if unculturable. Recent sequencing-based studies have charted oral ecosystems and how they change due to lifestyle or disease conditions. As studies progress, there is increasing evidence of an important role of the oral microbiome in diverse health conditions, which are not limited to diseases of the oral cavity. This, in turn, opens new avenues for microbiome-based diagnostics and therapeutics that benefit from the easy accessibility of the oral cavity for microbiome monitoring and manipulation. Yet, many challenges remain ahead. In this review, we survey the main sequencing-based methodologies that are currently used to explore the oral microbiome and highlight major findings enabled by these approaches. Finally, we discuss future prospects in the field.
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Affiliation(s)
- Jesse R. Willis
- Barcelona Supercomputing Centre (BCS-CNS), Jordi Girona, 29., 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), 08034 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), Jordi Girona, 29., 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Correspondence:
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Nguyen LN, Commault AS, Kahlke T, Ralph PJ, Semblante GU, Johir MAH, Nghiem LD. Genome sequencing as a new window into the microbial community of membrane bioreactors - A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135279. [PMID: 31791792 DOI: 10.1016/j.scitotenv.2019.135279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
Recent developed sequencing techniques have resulted in a new and unprecedented way to study biological wastewater treatment, in which most organisms are uncultivable. This review provides (i) an insight on state-of-the-art sequencing techniques and their limitations; (ii) a critical assessment of the microbial community in biological reactor and biofouling layer in a membrane bioreactor (MBR). The data from high-throughput sequencing has been used to infer microbial growth conditions and metabolisms of microorganisms present in MBRs at the time of sampling. These data shed new insight to two fundamental questions about a microbial community in the MBR process namely the microbial composition (who are they?) and the functions of each specific microbial assemblage (what are their function?). The results to date also highlight the complexity of the microbial community growing on MBRs. Environmental conditions are dynamic and diverse, and can influence the diversity and structural dynamics of any given microbial community for wastewater treatment. The benefits of understanding the structure of microbial communities on three major aspects of the MBR process (i.e. nutrient removal, biofouling control, and micropollutant removal) were symmetrically delineated. This review also indicates that the deployment of microbial community analysis for a practical engineering context, in terms of process design and system optimization, can be further realized.
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Affiliation(s)
- Luong N Nguyen
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia.
| | - Audrey S Commault
- Climate Change Cluster (C3), University of Technology Sydney, NSW 2007, Australia
| | - Tim Kahlke
- Climate Change Cluster (C3), University of Technology Sydney, NSW 2007, Australia
| | - Peter J Ralph
- Climate Change Cluster (C3), University of Technology Sydney, NSW 2007, Australia
| | - Galilee U Semblante
- Technical Services, Western Sydney University, Kingswood, NSW 2747, Australia
| | - Md Abu Hasan Johir
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, NSW 2007, Australia; NTT Institute of Hi-Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
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Saha J, Saha BK, Pal Sarkar M, Roy V, Mandal P, Pal A. Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes. Front Microbiol 2019; 10:2896. [PMID: 31921071 PMCID: PMC6928123 DOI: 10.3389/fmicb.2019.02896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/02/2019] [Indexed: 01/02/2023] Open
Abstract
Soil is a diversified and complex ecological niche, home to a myriad of microorganisms particularly bacteria. The physico-chemical complexities of soil results in a plethora of physiological variations to exist within the different types of soil dwelling bacteria, giving rise to a wide variation in genome structure and complexity. This serves as an attractive proposition to analyze and compare the genome of a large number soil bacteria to comprehend their genome complexity and evolution. In this study a combination of codon usage and molecular phylogenetics of the whole genome and key housekeeping genes like infB (translation initiation factor 2), trpB (tryptophan synthase, beta subunit), atpD (ATP synthase, beta subunit), and rpoB (RNA polymerase, beta subunit) of 92 soil bacterial species spread across the entire eubacterial domain and residing in different soil types was performed. The results indicated the direct relationship of genome size with codon bias and coding frequency in the studied bacteria. The codon usage profile demonstrated by the gene trpB was found to be relatively different from the rest of the housekeeping genes with a large number of bacteria having a greater percentage of genes with Nc values less than the Nc of trpB. The results from the overall codon usage bias profile also depicted that the codon usage bias in the key housekeeping genes of soil bacteria was majorly due to selectional pressure and not mutation. The analysis of hydrophobicity of the gene product encoded by the rpoB coding sequences demonstrated tight clustering across all the soil bacteria suggesting conservation of protein structure for maintenance of form and function. The phylogenetic affinities inferred using 16S rRNA gene and the housekeeping genes demonstrated conflicting signals with trpB gene being the noisiest one. The housekeeping gene atpD was found to depict the least amount of evolutionary change in the soil bacteria considered in this study except in two Clostridium species. The phylogenetic and codon usage analysis of the soil bacteria consistently demonstrated the relatedness of Azotobacter chroococcum with different species of the genus Pseudomonas.
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Affiliation(s)
- Jayanti Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Barnan K. Saha
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Monalisha Pal Sarkar
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Vivek Roy
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Parimal Mandal
- Mycology & Plant Pathology Laboratory, Department of Botany, Raiganj University, Raiganj, India
| | - Ayon Pal
- Microbiology & Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, India
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Connors E, Soto-Dávila M, Hossain A, Vasquez I, Gnanagobal H, Santander J. Identification and validation of reliable Aeromonas salmonicida subspecies salmonicida reference genes for differential gene expression analyses. INFECTION GENETICS AND EVOLUTION 2019; 73:314-321. [DOI: 10.1016/j.meegid.2019.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 01/19/2023]
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Ogier JC, Pagès S, Galan M, Barret M, Gaudriault S. rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing. BMC Microbiol 2019; 19:171. [PMID: 31357928 PMCID: PMC6664775 DOI: 10.1186/s12866-019-1546-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022] Open
Abstract
Background Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3 V4 hypervariable region of the 16S rRNA gene. Results We first designed universal primers for rpoB suitable for use with Illumina sequencing-based technology and constructed a reference rpoB database of 45,000 sequences. The rpoB and V3 V4 markers were amplified and sequenced from (i) a mock community of 19 bacterial strains from both Gram-negative and Gram-positive lineages; (ii) bacterial assemblages associated with entomopathogenic nematodes. In metabarcoding analyses of mock communities with two analytical pipelines (FROGS and DADA2), the estimated diversity captured with the rpoB marker resembled the expected composition of these mock communities more closely than that captured with V3 V4. The rpoB marker had a higher level of taxonomic affiliation, a higher sensitivity (detection of all the species present in the mock communities), and a higher specificity (low rates of spurious OTU detection) than V3 V4. We compared the performance of the rpoB and V3 V4 markers in an animal ecosystem model, the infective juveniles of the entomopathogenic nematode Steinernema glaseri carrying the symbiotic bacteria Xenorhabdus poinarii. Both markers showed the bacterial community associated with this nematode to be of low diversity (< 50 OTUs), but only rpoB reliably detected the symbiotic bacterium X. poinarii. Conclusions Our results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota. Further studies on other ecosystems should be considered to evaluate the universal usefulness of the rpoB marker. Our data highlight two crucial elements that should be taken into account to ensure more reliable and accurate descriptions of microbial diversity in high-throughput amplicon sequencing analyses: i) the need to include mock communities as controls; ii) the advantages of using a multigenic approach including at least one housekeeping gene (rpoB is a good candidate) and one variable region of the 16S rRNA gene. This study will be useful to the growing scientific community describing bacterial communities by metabarcoding in diverse ecosystems. Electronic supplementary material The online version of this article (10.1186/s12866-019-1546-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sylvie Pagès
- DGIMI, INRA, University Montpellier, 34095, Montpellier, France
| | - Maxime Galan
- CBGP INRA CIRAD IRD Montpellier SupAgro, Univ. Montpellier, 755 avenue du Campus Agropolis, CS 300 16, F-34988, Montferrier sur Lez cedex, France
| | - Matthieu Barret
- INRA AGROCAMPUS-Ouest, Universite d'Angers, Beaucouze, France
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Culbreath K, Melanson S, Gale J, Baker J, Li F, Saebo O, Kommedal O, Contreras D, Garner OB, Yang S. Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids. J Mol Diagn 2019; 21:913-923. [PMID: 31229651 DOI: 10.1016/j.jmoldx.2019.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 03/03/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing-based 16S rRNA gene metagenomic sequencing (16S MG) technology has tremendous potential for improving diagnosis of bacterial infections given its quantitative capability and culture-independent approach. We validated and used a quantitative 16S MG assay to identify and quantify bacterial species in clinical samples from a wide spectrum of infections, including meningitis, septic arthritis, brain abscess, intra-abdominal abscess, soft tissue abscess, and pneumonia. Twenty clinical samples were tested, and 16S MG identified a total of 34 species, compared with 22 species and three descriptive findings identified by culture. 16S MG results matched culture results in 75% (15/20) of the samples but detected at least one more species in five samples, including one culture-negative cerebrospinal fluid sample that was found to contain Streptococcus intermedius. Shotgun metagenomic sequencing verified the presence of all additional species. The 16S MG assay is highly sensitive, with a limit of detection of 10 to 100 colony-forming units/mL. Other performance characteristics, including linearity, precision, and specificity, all met the requirements for a clinical test. This assay showed the advantages of accurate identification and quantification of bacteria in culture-negative and polymicrobial infections for which conventional microbiology methods are limited. It also showed promises to serve unmet clinical needs for solving difficult infectious diseases cases.
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Affiliation(s)
- Karissa Culbreath
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; TriCore Reference Laboratories, Albuquerque, New Mexico
| | | | - James Gale
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Justin Baker
- TriCore Reference Laboratories, Albuquerque, New Mexico
| | - Fan Li
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California
| | | | - Oyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Deisy Contreras
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Omai B Garner
- Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
| | - Shangxin Yang
- Department of Pathlogy, University of New Mexico Health Sciences Center, Albuquerque, New Mexico; Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California.
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Nash MV, Anesio AM, Barker G, Tranter M, Varliero G, Eloe-Fadrosh EA, Nielsen T, Turpin-Jelfs T, Benning LG, Sánchez-Baracaldo P. Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol 2019; 94:5036517. [PMID: 29901729 PMCID: PMC6054269 DOI: 10.1093/femsec/fiy114] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/11/2018] [Indexed: 11/30/2022] Open
Abstract
Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonisation in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations. A key group of forefield diazotrophs, found throughout the forefields, was identified using a nifH phylogeny, associated with nifH Cluster I and III. Sequences related most closely to groups including Alphaproteobacteria, Betaproteobacteria, Cyanobacteria and Firmicutes. Using multiple nif genes in a Last Common Ancestor analysis revealed a diverse range of diazotrophs across the forefields. Key organisms identified across the forefields included Nostoc, Geobacter, Polaromonas and Frankia. Nitrogen fixers that are symbiotic with plants were also identified, through the presence of root associated diazotrophs, which fix nitrogen in return for reduced carbon. Additional nitrogen fixers identified in forefield soils were metabolically diverse, including fermentative and sulphur cycling bacteria, halophiles and anaerobes.
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Affiliation(s)
- Maisie V Nash
- School of Geographical Sciences, University of Bristol, UK
| | | | - Gary Barker
- School of Life Sciences, University of Bristol, UK
| | - Martyn Tranter
- School of Geographical Sciences, University of Bristol, UK
| | | | | | - Torben Nielsen
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, US
| | | | - Liane G Benning
- GFZ German Research Centre for Geosciences, Telegrafenenberg, 14473 Potsdam, Germany.,School of Earth and Environment, University of Leeds, LS2 9JT, Leeds, UK.,Department of Earth Sciences, Free University of Berlin, Malteserstr, 74-100, Building A, 12249, Berlin, Germany
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Charnock C, Hagen RX, Nguyen TNT, Vo LT. Diversion and phylogenetic relatedness of filterable bacteria from Norwegian tap and bottled waters. JOURNAL OF WATER AND HEALTH 2019; 17:295-307. [PMID: 30942779 DOI: 10.2166/wh.2019.284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Numerous articles have documented the existence of filterable bacteria. Where filtration is the chosen method of sterilization for medicinal or media components, these bacteria will by definition render products non-sterile. They may further represent a health hazard to the end user. A wide-range of bacterial genera were found in bottled and tap water filtrates from 0.2 μm filters, including genera housing opportunistic pathogens (e.g. Methylobacterium) and endospore formers (Paenibacillus). Two municipal tap water isolates were only distantly related to named species. One of these grew on agar, and could potentially provide hitherto unharvested useful biological products. The other grew only in water, and failed to produce colonies on media targeting either heterotrophs or autotrophs. The present study is one of very few looking at filterable bacteria in bottled waters intended for human consumption and the first identifying the filterable portion. It extends the range of known habitats of filterable bacteria and provides data on two new or novel species.
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Affiliation(s)
- Colin Charnock
- Department of Life Sciences and Health, Oslo Metropolitan University, NO-0130, Oslo, Norway E-mail:
| | - Ralf Xue Hagen
- Department of Life Sciences and Health, Oslo Metropolitan University, NO-0130, Oslo, Norway E-mail:
| | - Theresa Ngoc-Thu Nguyen
- Department of Life Sciences and Health, Oslo Metropolitan University, NO-0130, Oslo, Norway E-mail:
| | - Linh Thuy Vo
- Department of Life Sciences and Health, Oslo Metropolitan University, NO-0130, Oslo, Norway E-mail:
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Poirier S, Rué O, Peguilhan R, Coeuret G, Zagorec M, Champomier-Vergès MC, Loux V, Chaillou S. Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing. PLoS One 2018; 13:e0204629. [PMID: 30252901 PMCID: PMC6155546 DOI: 10.1371/journal.pone.0204629] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/11/2018] [Indexed: 12/21/2022] Open
Abstract
Meat and seafood spoilage ecosystems harbor extensive bacterial genomic diversity that is mainly found within a small number of species but within a large number of strains with different spoilage metabolic potential. To decipher the intraspecies diversity of such microbiota, traditional metagenetic analysis using the 16S rRNA gene is inadequate. We therefore assessed the potential benefit of an alternative genetic marker, gyrB, which encodes the subunit B of DNA gyrase, a type II DNA topoisomerase. A comparison between 16S rDNA-based (V3-V4) amplicon sequencing and gyrB-based amplicon sequencing was carried out in five types of meat and seafood products, with five mock communities serving as quality controls. Our results revealed that bacterial richness in these mock communities and food samples was estimated with higher accuracy using gyrB than using16S rDNA. However, for Firmicutes species, 35% of putative gyrB reads were actually identified as sequences of a gyrB paralog, parE, which encodes subunit B of topoisomerase IV; we therefore constructed a reference database of published sequences of both gyrB and pare for use in all subsequent analyses. Despite this co-amplification, the deviation between relative sequencing quantification and absolute qPCR quantification was comparable to that observed for 16S rDNA for all the tested species. This confirms that gyrB can be used successfully alongside 16S rDNA to determine the species composition (richness and evenness) of food microbiota. The major benefit of gyrB sequencing is its potential for improving taxonomic assignment and for further investigating OTU richness at the subspecies level, thus allowing more accurate discrimination of samples. Indeed, 80% of the reads of the 16S rDNA dataset were represented by thirteen 16S rDNA-based OTUs that could not be assigned at the species-level. Instead, these same clades corresponded to 44 gyrB-based OTUs, which differentiated various lineages down to the subspecies level. The increased ability of gyrB-based analyses to track and trace phylogenetically different groups of strains will generate improved resolution and more reliable results for studies of the strains implicated in food processes.
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Affiliation(s)
- Simon Poirier
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Rué
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Raphaëlle Peguilhan
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Gwendoline Coeuret
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stéphane Chaillou
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393-2411. [DOI: 10.1099/ijsem.0.002833] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Joseph S. Wirth
- Department of Microbiology, University of Georgia, Athens, GA, USA
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Pinevich AV, Andronov EE, Pershina EV, Pinevich AA, Dmitrieva HY. Testing culture purity in prokaryotes: criteria and challenges. Antonie van Leeuwenhoek 2018; 111:1509-1521. [PMID: 29488181 DOI: 10.1007/s10482-018-1054-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/21/2018] [Indexed: 01/05/2023]
Abstract
Reliance on pure cultures was introduced at the beginning of microbiology as a discipline and has remained significant although their adaptive properties are essentially dissimilar from those of mixed cultures and environmental populations. They are needed for (i) taxonomic identification; (ii) diagnostics of pathogens; (iii) virulence and pathogenicity studies; (iv) elucidation of metabolic properties; (v) testing sensitivity to antibiotics; (vi) full-length genome assembly; (vii) strain deposition in microbial collections; and (viii) description of new species with name validation. Depending on the specific task there are alternative claims for culture purity, i.e., when conventional criteria are satisfied or when looking deeper is necessary. Conventional proof (microscopic and plating controls) has a low resolution and depends on the observer's personal judgement. Phenotypic criteria alone cannot prove culture purity and should be complemented with genomic criteria. We consider the possible use of DNA high-throughput culture sequencing data to define criteria for only one genospecies, axenic state detection panel and only one genome. The second and third of these are preferable, although their resolving capacity (depth) is limited. Because minor contaminants may go undetected, even with deep sequencing, the reliably pure culture would be a clonal culture launched from a single cell or trichome (multicellular bacterium). Although this type of culture is associated with technical difficulties and cannot be employed on a large scale (the corresponding inoculums may have low chances of growth when transferred to solid media), it is hoped that the high-throughput culturing methods introduced by 'culturomics' will overcome this obstacle.
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Affiliation(s)
- Alexander V Pinevich
- Saint Petersburg State University, Universitetskaya Quay, 7/9, P.O. Box 199034, St. Petersburg, Russia.
| | - Eugeny E Andronov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Russian Academy of Sciences, Podbelskogo Highway, 3, P.O. Box 196608, St. Petersburg-Pushkin, Russia
| | - Elizaveta V Pershina
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Russian Academy of Sciences, Podbelskogo Highway, 3, P.O. Box 196608, St. Petersburg-Pushkin, Russia
| | - Agnia A Pinevich
- Saint Petersburg State University, Universitetskaya Quay, 7/9, P.O. Box 199034, St. Petersburg, Russia
| | - Helena Y Dmitrieva
- Saint Petersburg State University, Universitetskaya Quay, 7/9, P.O. Box 199034, St. Petersburg, Russia
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Louca S, Doebeli M, Parfrey LW. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. MICROBIOME 2018; 6:41. [PMID: 29482646 PMCID: PMC5828423 DOI: 10.1186/s40168-018-0420-9] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/30/2018] [Indexed: 05/13/2023]
Abstract
The 16S ribosomal RNA gene is the most widely used marker gene in microbial ecology. Counts of 16S sequence variants, often in PCR amplicons, are used to estimate proportions of bacterial and archaeal taxa in microbial communities. Because different organisms contain different 16S gene copy numbers (GCNs), sequence variant counts are biased towards clades with greater GCNs. Several tools have recently been developed for predicting GCNs using phylogenetic methods and based on sequenced genomes, in order to correct for these biases. However, the accuracy of those predictions has not been independently assessed. Here, we systematically evaluate the predictability of 16S GCNs across bacterial and archaeal clades, based on ∼ 6,800 public sequenced genomes and using several phylogenetic methods. Further, we assess the accuracy of GCNs predicted by three recently published tools (PICRUSt, CopyRighter, and PAPRICA) over a wide range of taxa and for 635 microbial communities from varied environments. We find that regardless of the phylogenetic method tested, 16S GCNs could only be accurately predicted for a limited fraction of taxa, namely taxa with closely to moderately related representatives (≲15% divergence in the 16S rRNA gene). Consistent with this observation, we find that all considered tools exhibit low predictive accuracy when evaluated against completely sequenced genomes, in some cases explaining less than 10% of the variance. Substantial disagreement was also observed between tools (R2<0.5) for the majority of tested microbial communities. The nearest sequenced taxon index (NSTI) of microbial communities, i.e., the average distance to a sequenced genome, was a strong predictor for the agreement between GCN prediction tools on non-animal-associated samples, but only a moderate predictor for animal-associated samples. We recommend against correcting for 16S GCNs in microbiome surveys by default, unless OTUs are sufficiently closely related to sequenced genomes or unless a need for true OTU proportions warrants the additional noise introduced, so that community profiles remain interpretable and comparable between studies.
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Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.
- Department of Zoology, University of British Columbia, Vancouver, Canada.
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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Almeida E, Serra CR, Albuquerque P, Guerreiro I, Teles AO, Enes P, Tavares F. Multiplex PCR identification and culture-independent quantification of Bacillus licheniformis by qPCR using specific DNA markers. Food Microbiol 2018; 74:1-10. [PMID: 29706322 DOI: 10.1016/j.fm.2018.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 12/29/2017] [Accepted: 02/17/2018] [Indexed: 11/26/2022]
Abstract
Probiotics benefits in fish farming have been usually inferred appraising the effects observed on the host and not through the direct assessment of probiotic dynamics in the host gut microbiota. To overcome this gap, quantitative PCR (qPCR) can be a powerful approach to study the bacterial dynamics in fish gut microbiota. The presented work proposes four B. licheniformis-specific DNA markers and details a qPCR method to track putative probiotics B. licheniformis on fish gut. The four B. licheniformis-specific DNA markers - BL5B (hypothetical protein BL00303), BL8A (serA2), BL13C (rfaB) and BL18A (ligD) - were selected and validated by PCR and multiplex-PCR with 20 B. licheniformis isolates and a broad range of non-target bacteria. To assess the dynamics of B. licheniformis in the digesta of farmed fish, a qPCR was validated using markers BL8A and BL18A and calibration curves obtained for both markers with digesta samples spiked with B. licheniformis cells showed a high correlation (R2 > 0.99) over 6 log units (CFU/reaction), and a limit of detection (LOD) as low as 247 CFUs/reaction. Furthermore, the consistent qPCR repeatability and reproducibility underline the specificity and reliability of the qPCR proposed. Ultimately, the possibility to monitor the dynamics of B. licheniformis probiotics in the gut microbiota of farmed fish might be instrumental to optimize best practices in aquaculture.
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Affiliation(s)
- Eduarda Almeida
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Edifício FC4 - Via Panorâmica nº 36, 4150-564 Porto, Portugal
| | - Cláudia R Serra
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Pedro Albuquerque
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Inês Guerreiro
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Edifício FC4 - Via Panorâmica nº 36, 4150-564 Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Aires Oliva Teles
- FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Edifício FC4 - Via Panorâmica nº 36, 4150-564 Porto, Portugal; CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Paula Enes
- CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Fernando Tavares
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; FCUP - Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Edifício FC4 - Via Panorâmica nº 36, 4150-564 Porto, Portugal.
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Devanga Ragupathi NK, Muthuirulandi Sethuvel DP, Inbanathan FY, Veeraraghavan B. Accurate differentiation of Escherichia coli and Shigella serogroups: challenges and strategies. New Microbes New Infect 2017; 21:58-62. [PMID: 29204286 PMCID: PMC5711669 DOI: 10.1016/j.nmni.2017.09.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/07/2017] [Accepted: 09/19/2017] [Indexed: 12/09/2022] Open
Abstract
Shigella spp. and Escherichia coli are closely related; both belong to the family Enterobacteriaceae. Phenotypically, Shigella spp. and E. coli share many common characteristics, yet they have separate entities in epidemiology and clinical disease, which poses a diagnostic challenge. We collated information for the best possible approach to differentiate clinically relevant E. coli from Shigella spp. We found that a molecular approach is required for confirmation. High discriminatory potential is seen with whole genome sequencing analysed for k-mers and single nucleotide polymorphism. Among these, identification using single nucleotide polymorphism is easy to perform and analyse, and it thus appears more promising. Among the nonmolecular methods, matrix-assisted desorption ionization–time of flight mass spectrometry may be applicable when data analysis is assisted with advanced analytic tools.
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Affiliation(s)
| | | | - F Y Inbanathan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - B Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
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Zhu Y, Hassan YI, Lepp D, Shao S, Zhou T. Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins. Toxins (Basel) 2017; 9:E130. [PMID: 28387743 PMCID: PMC5408204 DOI: 10.3390/toxins9040130] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 02/01/2023] Open
Abstract
Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification.
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Affiliation(s)
- Yan Zhu
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Yousef I Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Dion Lepp
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Suqin Shao
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
| | - Ting Zhou
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G5C9, Canada.
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It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research. Int J Mol Sci 2017; 18:ijms18040714. [PMID: 28350330 PMCID: PMC5412300 DOI: 10.3390/ijms18040714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/27/2022] Open
Abstract
There have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. However, "chimeric RNA" has never been lucidly defined, partly because "gene" itself is still ill-defined and because the means of production for many RNAs is unclear. Since the number of putative chimeras is soaring, it is imperative to establish a pellucid definition for it, in order to differentiate chimeras from regular RNAs. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. We propose that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas those RNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimeras. Many RNAs containing sequences of two neighboring genes may be transcribed via a readthrough mechanism, and thus are actually RNAs of unannotated genes or RNA variants of known genes, but not chimeras. In today's chimeric RNA research, there are still several key flaws, technical constraints and understudied tasks, which are also described in this perspective essay.
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Peng J, Wegner CE, Liesack W. Short-Term Exposure of Paddy Soil Microbial Communities to Salt Stress Triggers Different Transcriptional Responses of Key Taxonomic Groups. Front Microbiol 2017; 8:400. [PMID: 28400748 PMCID: PMC5368272 DOI: 10.3389/fmicb.2017.00400] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/27/2017] [Indexed: 11/30/2022] Open
Abstract
Soil salinization due to seawater intrusion along coastal areas is an increasing threat to rice cultivation worldwide. While the detrimental impact on rice growth and yield has been thoroughly studied, little is known about how severe salinity affects structure and function of paddy soil microbial communities. Here, we examined their short-term responses to half- and full-strength seawater salinity in controlled laboratory experiments. Slurry microcosms were incubated under anoxic conditions, with rice straw added as carbon source. Stress exposure time was for 2 days after a pre-incubation period of 7 days. Relative to the control, moderate (300 mM NaCl) and high (600 mM NaCl) salt stress suppressed both net consumption of acetate and methane production by 50% and 70%, respectively. Correspondingly, community-wide mRNA expression decreased by 50–65%, with significant changes in relative transcript abundance of family-level groups. mRNA turnover was clearly more responsive to salt stress than rRNA dynamics. Among bacteria, Clostridiaceae were most abundant and the only group whose transcriptional activity was strongly stimulated at 600 mM NaCl. In particular, clostridial mRNA involved in transcription/translation, fermentation, uptake and biosynthesis of compatible solutes, and flagellar motility was significantly enriched in response salt stress. None of the other bacterial groups were able to compete at 600 mM NaCl. Their responses to 300 mM NaCl were more diverse. Lachnospiraceae increased, Ruminococcaceae maintained, and Peptococcaceae, Veillonellaceae, and Syntrophomonadaceae decreased in relative mRNA abundance. Among methanogens, Methanosarcinaceae were most dominant. Relative to other family-level groups, salt stress induced a significant enrichment of transcripts related to the CO dehydrogenase/acetyl-coenzyme A synthase complex, methanogenesis, heat shock, ammonium uptake, and thermosomes, but the absolute abundance of methanosarcinal mRNA decreased. Most strikingly, the transcriptional activity of the Methanocellaceae was completely suppressed already at 300 mM NaCl. Apparently, the key taxonomic groups involved in the methanogenic breakdown of plant polymers significantly differ in their ability to cope with severe salt stress. Presumably, this different ability is directly linked to differences in their genetic potential and metabolic flexibility to reassign available energy resources for cellular adaptation to salt stress.
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Affiliation(s)
- Jingjing Peng
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
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Søborg DA, Hendriksen NB, Kilian M, Christensen JH, Kroer N. Bacterial Human Virulence Genes across Diverse Habitats As Assessed by In silico Analysis of Environmental Metagenomes. Front Microbiol 2016; 7:1712. [PMID: 27857707 PMCID: PMC5093120 DOI: 10.3389/fmicb.2016.01712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/12/2016] [Indexed: 01/18/2023] Open
Abstract
The occurrence and distribution of clinically relevant bacterial virulence genes across natural (non-human) environments is not well understood. We aimed to investigate the occurrence of homologs to bacterial human virulence genes in a variety of ecological niches to better understand the role of natural environments in the evolution of bacterial virulence. Twenty four bacterial virulence genes were analyzed in 46 diverse environmental metagenomic datasets, representing various soils, seawater, freshwater, marine sediments, hot springs, the deep-sea, hypersaline mats, microbialites, gutless worms and glacial ice. Homologs to 16 bacterial human virulence genes, involved in urinary tract infections, gastrointestinal diseases, skin diseases, and wound and systemic infections, showed global ubiquity. A principal component analysis did not demonstrate clear trends across the metagenomes with respect to occurrence and frequency of observed gene homologs. Full-length (>95%) homologs of several virulence genes were identified, and translated sequences of the environmental and clinical genes were up to 50-100% identical. Furthermore, phylogenetic analyses indicated deep branching positions of some of the environmental gene homologs, suggesting that they represent ancient lineages in the phylogeny of the clinical genes. Fifteen virulence gene homologs were detected in metatranscriptomes, providing evidence of environmental expression. The ubiquitous presence and transcription of the virulence gene homologs in non-human environments point to an important ecological role of the genes for the activity and survival of environmental bacteria. Furthermore, the high degree of sequence conservation between several of the environmental and clinical genes suggests common ancestral origins.
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Affiliation(s)
- Ditte A Søborg
- Department of Environmental Science, Aarhus UniversityRoskilde, Denmark; Research Group for Energy and Environment, VIA University CollegeHorsens, Denmark
| | - Niels B Hendriksen
- Department of Environmental Science, Aarhus University Roskilde, Denmark
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University Aarhus, Denmark
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Niels Kroer
- Department of Biology, University of Copenhagen Copenhagen, Denmark
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Lan Y, Rosen G, Hershberg R. Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains. MICROBIOME 2016; 4:18. [PMID: 27138046 PMCID: PMC4853863 DOI: 10.1186/s40168-016-0162-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 03/22/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels. RESULTS In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that the percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage. CONCLUSIONS Our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.
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Affiliation(s)
- Yemin Lan
- />School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 USA
| | - Gail Rosen
- />Ecological and Evolutionary Signal-processing and Informatics Laboratory, Electrical & Computer Engineering Department, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 USA
| | - Ruth Hershberg
- />Rachel & Menachem Mendelovitch Evolutionary Processes of Mutation & Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, 31096 Haifa, Israel
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Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State. Microbiol Res 2016; 188-189:23-33. [PMID: 27296959 DOI: 10.1016/j.micres.2016.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/16/2016] [Accepted: 04/21/2016] [Indexed: 12/11/2022]
Abstract
Yucatán State is dominated by two kinds of soil, named "Black Leptosol" and "Red Leptosol", which are interwoven across the State. In this work, we analyzed the relation between the edaphic characteristics and the bacterial and fungal community structures in these two kinds of Leptosol. The results revealed that Black Leptosol (BlaS) had a higher content of calcium carbonates, organic matter, nitrogen, and phosphorus than Red Leptosol (RedS). The most outstanding difference in the bacterial community structure between BlaS and RedS was that while in BlaS Actinobacteria was the most abundant phylum (43.7%), followed by Acidobacteria (26.9%) and Proteobacteria (23.6%), in RedS the bacterial community was strongly dominated by Acidobacteria (83%). Two fungal phyla were identified in both kinds of soil; Ascomycota, with 77% in BlaS and 56% in RedS, and Basidiomycota, with 22% in RedS and only 0.67% in BlaS. The most relevant difference between the two fungal communities was that excepting for Fusarium sp., all the species they had were different. Thus, in contrast with bacterial communities, where most of the major OTUs were present in both kinds of soil, fungal communities appeared to be unique to each kind of Leptosol.
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