1
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Wu R, Ji P, Hua Y, Li H, Zhang W, Wei Y. Research progress in isolation and identification of rumen probiotics. Front Cell Infect Microbiol 2024; 14:1411482. [PMID: 38836057 PMCID: PMC11148321 DOI: 10.3389/fcimb.2024.1411482] [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: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.
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Affiliation(s)
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | | | | | | | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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2
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Ma J, Sun H, Li B, Wu B, Zhang X, Ye L. Horizontal transfer potential of antibiotic resistance genes in wastewater treatment plants unraveled by microfluidic-based mini-metagenomics. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133493. [PMID: 38228000 DOI: 10.1016/j.jhazmat.2024.133493] [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: 09/11/2023] [Revised: 12/30/2023] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs), which can potentially spread to the environment and human populations. However, the extent and mechanisms of ARG transfer in WWTPs are not well understood due to the high microbial diversity and limitations of molecular techniques. In this study, we used a microfluidic-based mini-metagenomics approach to investigate the transfer potential and mechanisms of ARGs in activated sludge from WWTPs. Our results show that while diverse ARGs are present in activated sludge, only a few highly similar ARGs are observed across different taxa, indicating limited transfer potential. We identified two ARGs, ermF and tla-1, which occur in a variety of bacterial taxa and may have high transfer potential facilitated by mobile genetic elements. Interestingly, genes that are highly similar to the sequences of these two ARGs, as identified in this study, display varying patterns of abundance across geographic regions. Genes similar to ermF found are widely found in Asia and the Americas, while genes resembling tla-1 are primarily detected in Asia. Genes similar to both genes are barely detected in European WWTPs. These findings shed light on the limited horizontal transfer potential of ARGs in WWTPs and highlight the importance of monitoring specific ARGs in different regions to mitigate the spread of antibiotic resistance.
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Affiliation(s)
- Jiachen Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China; School of Environmental Science and Engineering, Changzhou University, Changzhou 213164, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Xuxiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
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3
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Bowers RM, Gonzalez-Pena V, Wardhani K, Goudeau D, Blow MJ, Udwary D, Klein D, Vill AC, Brito IL, Woyke T, Malmstrom R, Gawad C. scMicrobe PTA: Near Complete Genomes from Single Bacterial Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.577819. [PMID: 38352480 PMCID: PMC10862798 DOI: 10.1101/2024.01.30.577819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Microbial genomes produced by single-cell amplification are largely incomplete. Here, we show that primary template amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard amplification approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
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Affiliation(s)
- Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Kartika Wardhani
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Danielle Goudeau
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew James Blow
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Klein
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Charles Gawad
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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4
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Jitsuno K, Hoshino T, Nishikawa Y, Kogawa M, Mineta K, Strasser M, Ikehara K, Everest J, Maeda L, Inagaki F, Takeyama H. Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere. mSphere 2024; 9:e0033723. [PMID: 38170974 PMCID: PMC10826368 DOI: 10.1128/msphere.00337-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Deep-sea and subseafloor sedimentary environments host heterotrophic microbial communities that contribute to Earth's carbon cycling. However, the potential metabolic functions of individual microorganisms and their biogeographical distributions in hadal ocean sediments remain largely unexplored. In this study, we conducted single-cell genome sequencing on sediment samples collected from six sites (7,445-8,023 m water depth) along an approximately 500 km transect of the Japan Trench during the International Ocean Discovery Program Expedition 386. A total of 1,886 single-cell amplified genomes (SAGs) were obtained, offering comprehensive genetic insights into sedimentary microbial communities in surface sediments (<1 m depth) above the sulfate-methane transition zone along the Japan Trench. Our genome data set included 269 SAGs from Atribacterota JS1, the predominant bacterial clade in these hadal environments. Phylogenetic analysis classified SAGs into nine distinct phylotypes, whereas metagenome-assembled genomes were categorized into only two phylotypes, advancing JS1 diversity coverage through a single cell-based approach. Comparative genomic analysis of JS1 lineages from different habitats revealed frequent detection of genes related to organic carbon utilization, such as extracellular enzymes like clostripain and α-amylase, and ABC transporters of oligopeptide from Japan Trench members. Furthermore, specific JS1 phylotypes exhibited a strong correlation with in situ methane concentrations and contained genes involved in glycine betaine metabolism. These findings suggest that the phylogenomically diverse and novel Atribacterota JS1 is widely distributed in Japan Trench sediment, playing crucial roles in carbon cycling within the hadal sedimentary biosphere.IMPORTANCEThe Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.
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Affiliation(s)
- Kana Jitsuno
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Yohei Nishikawa
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Masato Kogawa
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Katsuhiko Mineta
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Marine Open Innovation Institute, Shizuoka, Japan
| | - Michael Strasser
- Department of Geology, University of Innsbruck, Innsbruck, Austria
| | - Ken Ikehara
- Research Institute of Geology and Geoinformation, AIST Geological Survey of Japan, Tsukuba, Japan
| | | | - Lena Maeda
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
| | - Fumio Inagaki
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Haruko Takeyama
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - IODP Expedition 386 ScientistsBellanovaPieroBrunetMorganeCaiZhirongCattaneoAntonioHochmuthKatharinaHsiungKanhsiIshizawaTakashiItakiTakuyaJitsunoKanaJohnsonJoelKanamatsuToshiyaKeepMyraKiokaArataMaerzChristianMcHughCeciliaMicallefAaronMinLuoPandeyDhananjaiProustJean NoelRasburyTroyRiedingerNataschaBaoRuiSatoguchiYasufumiSawyerDerekSeibertChloeSilverMaxwellStraubSusanneVirtasaloJoonasWangYonghongWuTing-WeiZellersSarahKöllingMartinHuangJyh-Jaan StevenNagahashiYoshitaka
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- CBBD-OIL, AIST-Waseda University, Shinjuku-ku, Tokyo, Japan
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
- Research organization for Nano and Life Innovation, Waseda University, Shinjuku-ku, Tokyo, Japan
- Marine Open Innovation Institute, Shizuoka, Japan
- Department of Geology, University of Innsbruck, Innsbruck, Austria
- Research Institute of Geology and Geoinformation, AIST Geological Survey of Japan, Tsukuba, Japan
- British Geological Survey, Edinburgh, United Kingdom
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
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Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024; 17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.
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Affiliation(s)
- Klara Cerk
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Chabname Ghassemi Nedjad
- Inria, University of Bordeaux, INRAETalenceFrance
- University of Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800TalenceFrance
| | - Maxime Lecomte
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE STLO¸University of RennesRennesFrance
| | | | | | - Falk Hildebrand
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Simon Labarthe
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE, University of Bordeaux, BIOGECO, UMR 1202CestasFrance
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6
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Bowers RM, Gonzalez-Pena V, Wardhani K, Goudeau D, Blow MJ, Udwary D, Klein D, Vill AC, Brito IL, Woyke T, Malmstrom RR, Gawad C. scMicrobe PTA: near complete genomes from single bacterial cells. ISME COMMUNICATIONS 2024; 4:ycae085. [PMID: 39021442 PMCID: PMC11253033 DOI: 10.1093/ismeco/ycae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/05/2024] [Indexed: 07/20/2024]
Abstract
Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
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Affiliation(s)
- Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | | | - Kartika Wardhani
- Department of Pediatrics, Stanford University, Stanford, CA, United States
| | - Danielle Goudeau
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Matthew James Blow
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David Klein
- Department of Pediatrics, Stanford University, Stanford, CA, United States
| | - Albert C Vill
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Ilana L Brito
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rex R Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Charles Gawad
- Department of Pediatrics, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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7
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Wiegand S, Sobol M, Schnepp-Pesch LK, Yan G, Iqbal S, Vollmers J, Müller JA, Kaster AK. Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes. Microorganisms 2023; 11:2612. [PMID: 37894270 PMCID: PMC10608941 DOI: 10.3390/microorganisms11102612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.
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Affiliation(s)
| | | | | | | | | | | | | | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG 5), Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany; (S.W.); (M.S.); (L.K.S.-P.); (G.Y.); (S.I.); (J.V.); (J.A.M.)
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8
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Akaçin İ, Ersoy Ş, Doluca O, Güngörmüşler M. Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH 2 production. Sci Rep 2023; 13:17025. [PMID: 37813931 PMCID: PMC10562470 DOI: 10.1038/s41598-023-44357-3] [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: 04/14/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023] Open
Abstract
The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.
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Affiliation(s)
- İlayda Akaçin
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Şeymanur Ersoy
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Osman Doluca
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
- Department of Biomedical Engineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Mine Güngörmüşler
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
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Madhu B, Miller BM, Levy M. Single-cell analysis and spatial resolution of the gut microbiome. Front Cell Infect Microbiol 2023; 13:1271092. [PMID: 37860069 PMCID: PMC10582963 DOI: 10.3389/fcimb.2023.1271092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/11/2023] [Indexed: 10/21/2023] Open
Abstract
Over the past decade it has become clear that various aspects of host physiology, metabolism, and immunity are intimately associated with the microbiome and its interactions with the host. Specifically, the gut microbiome composition and function has been shown to play a critical role in the etiology of different intestinal and extra-intestinal diseases. While attempts to identify a common pattern of microbial dysbiosis linked with these diseases have failed, multiple studies show that bacterial communities in the gut are spatially organized and that disrupted spatial organization of the gut microbiome is often a common underlying feature of disease pathogenesis. As a result, focus over the last few years has shifted from analyzing the diversity of gut microbiome by sequencing of the entire microbial community, towards understanding the gut microbiome in spatial context. Defining the composition and spatial heterogeneity of the microbiome is critical to facilitate further understanding of the gut microbiome ecology. Development in single cell genomics approach has advanced our understanding of microbial community structure, however, limitations in approaches exist. Single cell genomics is a very powerful and rapidly growing field, primarily used to identify the genetic composition of microbes. A major challenge is to isolate single cells for genomic analyses. This review summarizes the different approaches to study microbial genomes at single-cell resolution. We will review new techniques for microbial single cell sequencing and summarize how these techniques can be applied broadly to answer many questions related to the microbiome composition and spatial heterogeneity. These methods can be used to fill the gaps in our understanding of microbial communities.
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Affiliation(s)
| | | | - Maayan Levy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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10
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Moreno IJ, Brahamsha B, Donia MS, Palenik B. Diverse Microbial Hot Spring Mat Communities at Black Canyon of the Colorado River. MICROBIAL ECOLOGY 2023; 86:1534-1551. [PMID: 36757423 PMCID: PMC10497668 DOI: 10.1007/s00248-023-02186-x] [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: 07/15/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The thermophilic microbial mat communities at hot springs in the Black Canyon of the Colorado River, thought to harbor the protistan human pathogen Naegleria fowleri, were surveyed using both culture-independent and -dependent methods to further understand the ecology of these hot spring microbiomes. Originating from Lake Mead source water, seven spring sites were sampled, varying in temperature from 25 to 55 °C. Amplicon-based high-throughput sequencing of twelve samples using 16S rRNA primers (hypervariable V4 region) revealed that most mats are dominated by cyanobacterial taxa, some but not all similar to those dominating the mats at other studied hot spring systems. 18S rRNA amplicon sequencing (V9 region) demonstrated a diverse community of protists and other eukaryotes including a highly abundant amoebal sequence related to Echinamoeba thermarum. Additional taxonomic and diversity metric analyses using near full-length 16S and 18S rRNA gene sequencing allowed a higher sequence-based resolution of the community. The mat sequence data suggest a major diversification of the cyanobacterial orders Leptolyngbyales, as well as microdiversity among several cyanobacterial taxa. Cyanobacterial isolates included some representatives of ecologically abundant taxa. A Spearman correlation analysis of short-read amplicon sequencing data supported the co-occurrences of populations of cyanobacteria, chloroflexi, and bacteroidetes providing evidence of common microbial co-occurrences across the Black Canyon hot springs.
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Affiliation(s)
- Ivan J Moreno
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Bianca Brahamsha
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
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11
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Ho H, Chovatia M, Egan R, He G, Yoshinaga Y, Liachko I, O’Malley R, Wang Z. Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning. PeerJ 2023; 11:e16129. [PMID: 37753177 PMCID: PMC10519199 DOI: 10.7717/peerj.16129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/28/2023] [Indexed: 09/28/2023] Open
Abstract
Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is often low in datasets with a small number of samples due to a lack of robust species co-abundance information. In this study, we exploited the chromatin conformation information obtained from Hi-C sequencing and developed a new reference-independent algorithm, Metagenome Binning with Abundance and Tetra-nucleotide frequencies-Long Range (metaBAT-LR), to improve the binning completeness of these datasets. This self-supervised algorithm builds a model from a set of high-quality genome bins to predict scaffold pairs that are likely to be derived from the same genome. Then, it applies these predictions to merge incomplete genome bins, as well as recruit unbinned scaffolds. We validated metaBAT-LR's ability to bin-merge and recruit scaffolds on both synthetic and real-world metagenome datasets of varying complexity. Benchmarking against similar software tools suggests that metaBAT-LR uncovers unique bins that were missed by all other methods. MetaBAT-LR is open-source and is available at https://bitbucket.org/project-metabat/metabat-lr.
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Affiliation(s)
- Harrison Ho
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
- School of Natural Sciences, University of California, Merced, CA, United States
| | - Mansi Chovatia
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Rob Egan
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Guifen He
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | | | - Ronan O’Malley
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Zhong Wang
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, United States
- School of Natural Sciences, University of California, Merced, CA, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, United States
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12
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Němečková K, Mareš J, Procházková L, Culka A, Košek F, Wierzchos J, Nedbalová L, Dudák J, Tymlová V, Žemlička J, Kust A, Zima J, Nováková E, Jehlička J. Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition. Front Microbiol 2023; 14:1175066. [PMID: 37485515 PMCID: PMC10359912 DOI: 10.3389/fmicb.2023.1175066] [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: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 07/25/2023] Open
Abstract
In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.
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Affiliation(s)
- Kateřina Němečková
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Mareš
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- Center Algatech, Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czechia
| | - Lenka Procházková
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Adam Culka
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Filip Košek
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Linda Nedbalová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Dudák
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Veronika Tymlová
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Jan Žemlička
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Andreja Kust
- Department of Earth and Planetary Science, University of Berkeley, Berkeley, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jan Zima
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan Jehlička
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
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13
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Anstett J, Plominsky AM, DeLong EF, Kiesser A, Jürgens K, Morgan-Lang C, Stepanauskas R, Stewart FJ, Ulloa O, Woyke T, Malmstrom R, Hallam SJ. A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters. Sci Data 2023; 10:332. [PMID: 37244914 DOI: 10.1038/s41597-023-02222-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/10/2023] [Indexed: 05/29/2023] Open
Abstract
Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.
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Affiliation(s)
- Julia Anstett
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Alvaro M Plominsky
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Alyse Kiesser
- School of Engineering, The University of British Columbia, Kelowna, BC, Canada
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, 4070386, Concepción, Chile
- Instituto Milenio de Oceanografía, Casilla 1313, 4070386, Concepción, Chile
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven J Hallam
- Graduate Program in Genome Sciences and Technology, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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14
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Nishikawa Y, Kogawa M, Hosokawa M, Wagatsuma R, Mineta K, Takahashi K, Ide K, Yura K, Behzad H, Gojobori T, Takeyama H. Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater. ISME COMMUNICATIONS 2022; 2:92. [PMID: 37938694 PMCID: PMC9723564 DOI: 10.1038/s43705-022-00179-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 04/26/2023]
Abstract
Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1-25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.
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Affiliation(s)
- Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masato Kogawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Ryota Wagatsuma
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Katsuhiko Mineta
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Kai Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Keigo Ide
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kei Yura
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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15
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Bawn M, Hernandez J, Trampari E, Thilliez G, Quince C, Webber MA, Kingsley RA, Hall N, Macaulay IC. Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella. Microb Genom 2022; 8. [PMID: 36125951 DOI: 10.1099/mgen.0.000871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Single cell approaches are increasingly used to study clonal evolution in human ageing and cancer but have not yet been deployed to study evolving clonal microbial populations. Here, we present an approach for single bacterial genomic analysis for in vitro evolution experiments using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing. We apply this to the experimental evolution of a hypermutator strain of Salmonella in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from populations we identified the presence and prevalence of sub-populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. We were also able to identify that the population exposed to antibiotic stress was able to develop resistance whilst maintaining diversity. This population structure could not be resolved from bulk sequence data, and our results show how high-throughput single-cell sequencing can enhance experimental studies of bacterial evolution.
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Affiliation(s)
- Matt Bawn
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | | | - Gaetan Thilliez
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Christopher Quince
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mark A Webber
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK.,Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UA, UK
| | - Robert A Kingsley
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
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16
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Kawaka F. Characterization of symbiotic and nitrogen fixing bacteria. AMB Express 2022; 12:99. [PMID: 35907164 PMCID: PMC9339069 DOI: 10.1186/s13568-022-01441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
Symbiotic nitrogen fixing bacteria comprise of diverse species associated with the root nodules of leguminous plants. Using an appropriate taxonomic method to confirm the identity of superior and elite strains to fix nitrogen in legume crops can improve sustainable global food and nutrition security. The current review describes taxonomic methods preferred and commonly used to characterize symbiotic bacteria in the rhizosphere. Peer reviewed, published and unpublished articles on techniques used for detection, classification and identification of symbiotic bacteria were evaluated by exploring their advantages and limitations. The findings showed that phenotypic and cultural techniques are still affordable and remain the primary basis of species classification despite their challenges. Development of new, robust and informative taxonomic techniques has really improved characterization and identification of symbiotic bacteria and discovery of novel and new species that are effective in biological nitrogen fixation (BNF) in diverse conditions and environments.
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Affiliation(s)
- Fanuel Kawaka
- Department of Biological Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O. Box 210-40601, Bondo, Kenya.
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