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Tothero GK, Hoover RL, Farag IF, Kaplan DI, Weisenhorn P, Emerson D, Chan CS. Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon. Appl Environ Microbiol 2024:e0059924. [PMID: 39133000 DOI: 10.1128/aem.00599-24] [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: 03/29/2024] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Leptothrix ochracea creates distinctive iron-mineralized mats that carpet streams and wetlands. Easily recognized by its iron-mineralized sheaths, L. ochracea was one of the first microorganisms described in the 1800s. Yet it has never been isolated and does not have a complete genome sequence available, so key questions about its physiology remain unresolved. It is debated whether iron oxidation can be used for energy or growth and if L. ochracea is an autotroph, heterotroph, or mixotroph. To address these issues, we sampled L. ochracea-rich mats from three of its typical environments (a stream, wetlands, and a drainage channel) and reconstructed nine high-quality genomes of L. ochracea from metagenomes. These genomes contain iron oxidase genes cyc2 and mtoA, showing that L. ochracea has the potential to conserve energy from iron oxidation. Sox genes confer potential to oxidize sulfur for energy. There are genes for both carbon fixation (RuBisCO) and utilization of sugars and organic acids (acetate, lactate, and formate). In silico stoichiometric metabolic models further demonstrated the potential for growth using sugars and organic acids. Metatranscriptomes showed a high expression of genes for iron oxidation; aerobic respiration; and utilization of lactate, acetate, and sugars, as well as RuBisCO, supporting mixotrophic growth in the environment. In summary, our results suggest that L. ochracea has substantial metabolic flexibility. It is adapted to iron-rich, organic carbon-containing wetland niches, where it can thrive as a mixotrophic iron oxidizer by utilizing both iron oxidation and organics for energy generation and both inorganic and organic carbon for cell and sheath production. IMPORTANCE Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea, which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.
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Affiliation(s)
- Gracee K Tothero
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Rene L Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Ibrahim F Farag
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - Daniel I Kaplan
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, USA
| | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Clara S Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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2
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Rose SA, Robicheau BM, Tolman J, Fonseca-Batista D, Rowland E, Desai D, Ratten JM, Kantor EJH, Comeau AM, Langille MG, Jerlström-Hultqvist J, Devred E, Sarthou G, Bertrand EM, LaRoche J. Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni. SCIENCE ADVANCES 2024; 10:eadn1476. [PMID: 39083619 PMCID: PMC11290528 DOI: 10.1126/sciadv.adn1476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.
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Affiliation(s)
- Sonja A. Rose
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Tolman
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Debany Fonseca-Batista
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Dhwani Desai
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jenni-Marie Ratten
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ella Joy H. Kantor
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - André M. Comeau
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Morgan G.I. Langille
- Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Emmanuel Devred
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Halifax, Nova Scotia, Canada
| | | | - Erin M. Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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3
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De La Cruz KF, Townsend EC, Alex Cheong JZ, Salamzade R, Liu A, Sandstrom S, Davila E, Huang L, Xu KH, Wu SY, Meudt JJ, Shanmuganayagam D, Gibson ALF, Kalan LR. The porcine skin microbiome exhibits broad fungal antagonism. Fungal Genet Biol 2024; 173:103898. [PMID: 38815692 DOI: 10.1016/j.fgb.2024.103898] [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: 01/12/2024] [Revised: 05/02/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
The skin and its microbiome function to protect the host from pathogen colonization and environmental stressors. In this study, using the Wisconsin Miniature Swine™ model, we characterize the porcine skin fungal and bacterial microbiomes, identify bacterial isolates displaying antifungal activity, and use whole-genome sequencing to identify biosynthetic gene clusters encoding for secondary metabolites that may be responsible for the antagonistic effects on fungi. Through this comprehensive approach of paired microbiome sequencing with culturomics, we report the discovery of novel species of Corynebacterium and Rothia. Further, this study represents the first comprehensive evaluation of the porcine skin mycobiome and the evaluation of bacterial-fungal interactions on this surface. Several diverse bacterial isolates exhibit potent antifungal properties against opportunistic fungal pathogens in vitro. Genomic analysis of inhibitory species revealed a diverse repertoire of uncharacterized biosynthetic gene clusters suggesting a reservoir of novel chemical and biological diversity. Collectively, the porcine skin microbiome represents a potential unique source of novel antifungals.
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Affiliation(s)
- Karinda F De La Cruz
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Elizabeth C Townsend
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States; Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - J Z Alex Cheong
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Rauf Salamzade
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Aiping Liu
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Evelin Davila
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; National Summer Undergraduate Research Project, University of Arizona, Tucson, AZ, United States
| | - Lynda Huang
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Kayla H Xu
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Sherrie Y Wu
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jennifer J Meudt
- Department of Animal & Dairy Sciences, University of Wisconsin, Madison, WI, United States; Center for Biomedical Swine Research & Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Department of Animal & Dairy Sciences, University of Wisconsin, Madison, WI, United States; Center for Biomedical Swine Research & Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Angela L F Gibson
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
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Salazar-Jaramillo L, de la Cuesta-Zuluaga J, Chica LA, Cadavid M, Ley RE, Reyes A, Escobar JS. Gut microbiome diversity within Clostridia is negatively associated with human obesity. mSystems 2024:e0062724. [PMID: 39012154 DOI: 10.1128/msystems.00627-24] [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: 05/03/2024] [Accepted: 06/06/2024] [Indexed: 07/17/2024] Open
Abstract
Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production. IMPORTANCE The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.
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Affiliation(s)
- Laura Salazar-Jaramillo
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | | | - Luis A Chica
- Department of Biological Sciences, Max Planck Tandem Group in Computational Biology, Research Group in Computational Biology and Microbial Ecology (BCEM), Universidad de los Andes, Bogota, Colombia
| | - María Cadavid
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Alejandro Reyes
- Department of Biological Sciences, Max Planck Tandem Group in Computational Biology, Research Group in Computational Biology and Microbial Ecology (BCEM), Universidad de los Andes, Bogota, Colombia
- Department of Pathology and Immunology, Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Juan S Escobar
- Vidarium-Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
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5
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Pinto Y, Bhatt AS. Sequencing-based analysis of microbiomes. Nat Rev Genet 2024:10.1038/s41576-024-00746-6. [PMID: 38918544 DOI: 10.1038/s41576-024-00746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/27/2024]
Abstract
Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease. The study of microbiomes has been facilitated by recent technological and analytical advances, such as cheaper and higher-throughput DNA and RNA sequencing, improved long-read sequencing and innovative computational analysis methods. These advances are providing a deeper understanding of microbiomes at the genomic, transcriptional and translational level, generating insights into their function and composition at resolutions beyond the species level.
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Affiliation(s)
- Yishay Pinto
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA.
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6
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Tian L, Fang G, Li G, Li L, Zhang T, Mao Y. Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human. MICROBIOME 2024; 12:107. [PMID: 38877573 PMCID: PMC11179227 DOI: 10.1186/s40168-024-01824-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/26/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health. RESULTS The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer. CONCLUSIONS The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.
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Affiliation(s)
- Li Tian
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Guimei Fang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Guijie Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Liguan Li
- The University of Hong Kong Shenzhen Institute of Research and Innovation, HKU SIRI, Shenzhen, Guangdong, 518057, China
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China
| | - Tong Zhang
- The University of Hong Kong Shenzhen Institute of Research and Innovation, HKU SIRI, Shenzhen, Guangdong, 518057, China
- Department of Civil Engineering, Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, The University of Hong Kong, Hong Kong SAR, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China.
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Zhang L, Lin TY, Liu WT, Ling F. Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification. ACS ENVIRONMENTAL AU 2024; 4:127-141. [PMID: 38765059 PMCID: PMC11100324 DOI: 10.1021/acsenvironau.3c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 05/21/2024]
Abstract
Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.
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Affiliation(s)
- Lin Zhang
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tzu-Yu Lin
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Wen-Tso Liu
- Department
of Civil and Environmental Engineering, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Wei X, Tsai MS, Liang L, Jiang L, Hung CJ, Jelliffe-Pawlowski L, Rand L, Snyder M, Jiang C. Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process. Cell Rep 2024; 43:114078. [PMID: 38598334 DOI: 10.1016/j.celrep.2024.114078] [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: 09/15/2023] [Revised: 03/01/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.
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Affiliation(s)
- Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Ming-Shian Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liang Liang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liuyiqi Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Chia-Jui Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Larry Rand
- Department of Obstetrics, Gynecology & Reproductive Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.
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9
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Liang JL, Feng SW, Lu JL, Wang XN, Li FL, Guo YQ, Liu SY, Zhuang YY, Zhong SJ, Zheng J, Wen P, Yi X, Jia P, Liao B, Shu WS, Li JT. Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages. Nat Commun 2024; 15:2827. [PMID: 38565528 PMCID: PMC10987575 DOI: 10.1038/s41467-024-47214-7] [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: 08/15/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.
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Affiliation(s)
- Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xiao-Nan Wang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Feng-Lin Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Yu-Qian Guo
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Shen-Yan Liu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Yuan-Yue Zhuang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Sheng-Ji Zhong
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jin Zheng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Ping Wen
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
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10
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Hollender M, Sałek M, Karlicki M, Karnkowska A. Single-cell genomics revealed Candidatus Grellia alia sp. nov. as an endosymbiont of Eutreptiella sp. (Euglenophyceae). Protist 2024; 175:126018. [PMID: 38325049 DOI: 10.1016/j.protis.2024.126018] [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: 09/12/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/09/2024]
Abstract
Though endosymbioses between protists and prokaryotes are widespread, certain host lineages have received disproportionate attention what may indicate either a predisposition to such interactions or limited studies on certain protist groups due to lack of cultures. The euglenids represent one such group in spite of microscopic observations showing intracellular bacteria in some strains. Here, we perform a comprehensive molecular analysis of a previously identified endosymbiont in the Eutreptiella sp. CCMP3347 using a single cell approach and bulk culture sequencing. The genome reconstruction of this endosymbiont allowed the description of a new endosymbiont Candidatus Grellia alia sp. nov. from the family Midichloriaceae. Comparative genomics revealed a remarkably complete conjugative type IV secretion system present in three copies on the plasmid sequences of the studied endosymbiont, a feature missing in the closely related Grellia incantans. This study addresses the challenge of limited host cultures with endosymbionts by showing that the genomes of endosymbionts reconstructed from single host cells have the completeness and contiguity that matches or exceeds those coming from bulk cultures. This paves the way for further studies of endosymbionts in euglenids and other protist groups. The research also provides the opportunity to study the diversity of endosymbionts in natural populations.
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Affiliation(s)
- Metody Hollender
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Marta Sałek
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland.
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11
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Peoples LM, Seixas MH, Evans KA, Bilbrey EM, Ranieri JR, Tappenbeck TH, Dore JE, Baumann A, Church MJ. Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake. Environ Microbiol 2024; 26:e16616. [PMID: 38517638 DOI: 10.1111/1462-2920.16616] [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: 11/11/2023] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.
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Affiliation(s)
- Logan M Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Miranda H Seixas
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Evan M Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - John R Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Tyler H Tappenbeck
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Adam Baumann
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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12
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Voutsinos MY, West-Roberts JA, Sachdeva R, Moreau JW, Banfield JF. Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes. BMC Biol 2024; 22:41. [PMID: 38369453 PMCID: PMC10875860 DOI: 10.1186/s12915-024-01841-0] [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: 06/29/2023] [Accepted: 02/07/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood. RESULTS Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems. CONCLUSIONS Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.
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Affiliation(s)
- Marcos Y Voutsinos
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacob A West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Rohan Sachdeva
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, UK
| | - Jillian F Banfield
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, Melbourne, VIC, Australia.
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
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13
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Sharko FS, Mazloum A, Krotova AO, Byadovskaya OP, Prokhvatilova LB, Chvala IA, Zolotikov UE, Kozlova AD, Krylova AS, Grosfeld EV, Prokopenko AV, Korzhenkov AA, Patrushev MV, Namsaraev ZB, Sprygin AV, Toshchakov SV. Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts. Front Vet Sci 2024; 11:1321202. [PMID: 38420205 PMCID: PMC10899707 DOI: 10.3389/fvets.2024.1321202] [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: 10/16/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction It has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis. Methods In this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus. Results The analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified. Discussion This study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained.
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Affiliation(s)
- Fedor S. Sharko
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Ali Mazloum
- Federal Center for Animal Health FGBI ARRIAH, Vladimir, Russia
| | | | | | | | - Ilya A. Chvala
- Federal Center for Animal Health FGBI ARRIAH, Vladimir, Russia
| | | | | | | | - Erika V. Grosfeld
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, Dolgoprudny, Russia
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14
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Rohwer RR, Kirkpatrick M, Garcia SL, Kellom M, McMahon KD, Baker BJ. Bacterial ecology and evolution converge on seasonal and decadal scales. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579087. [PMID: 38370794 PMCID: PMC10871203 DOI: 10.1101/2024.02.06.579087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum.
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Affiliation(s)
- Robin R. Rohwer
- The University of Texas at Austin, Department of Integrative Biology, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Mark Kirkpatrick
- The University of Texas at Austin, Department of Integrative Biology, 2415 Speedway #C0930, Austin, TX 78712, USA
| | - Sarahi L. Garcia
- Carl von Ossietzky Universität Oldenburg, Institute for Chemistry and Biology of the Marine Environment (ICBM), 26129 Oldenburg, Germany
- Stockholm University, Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, 106 91 Stockholm, Sweden
| | - Matthew Kellom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Katherine D. McMahon
- University of Wisconsin-Madison, Department of Bacteriology, 1550 Linden Drive, Madison, WI, 53706, USA
- University of Wisconsin-Madison, Department of Civil and Environmental Engineering, 1550 Linden Drive, Madison, WI, 53706, USA
| | - Brett J. Baker
- The University of Texas at Austin, Department of Integrative Biology, 2415 Speedway #C0930, Austin, TX 78712, USA
- The University of Texas at Austin, Department of Marine Science, Port Aransas, Austin, TX 78373, USA
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15
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Lindner BG, Gerhardt K, Feistel DJ, Rodriguez-R LM, Hatt JK, Konstantinidis KT. A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection. Int J Food Microbiol 2024; 410:110488. [PMID: 38035404 DOI: 10.1016/j.ijfoodmicro.2023.110488] [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: 05/17/2023] [Revised: 09/15/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.
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Affiliation(s)
- Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kenji Gerhardt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dorian J Feistel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- Department of Microbiology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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16
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Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, Konstantinidis KT. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio 2024; 15:e0269623. [PMID: 38085031 PMCID: PMC10790751 DOI: 10.1128/mbio.02696-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/03/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.
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Affiliation(s)
- Luis M. Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Roth E. Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tomeu Viver
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Dorian J. Feistel
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Blake G. Lindner
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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17
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Dong Q, Hua D, Wang X, Jiao Y, Liu L, Deng Q, Wu T, Zou H, Zhao C, Wang C, Reng J, Ding L, Hu S, Shi J, Wang Y, Zhang H, Sheng Y, Sun W, Shen Y, Tang L, Kong X, Chen L. Temporal colonization and metabolic regulation of the gut microbiome in neonatal oxen at single nucleotide resolution. THE ISME JOURNAL 2024; 18:wrad022. [PMID: 38365257 PMCID: PMC10833086 DOI: 10.1093/ismejo/wrad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/19/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The colonization of microbes in the gut is key to establishing a healthy host-microbiome symbiosis for newborns. We longitudinally profiled the gut microbiome in a model consisting of 36 neonatal oxen from birth up to 2 months postpartum and carried out microbial transplantation to reshape their gut microbiome. Genomic reconstruction of deeply sequenced fecal samples resulted in a total of 3931 metagenomic-assembled genomes from 472 representative species, of which 184 were identified as new species when compared with existing databases of oxen. Single nucleotide level metagenomic profiling shows a rapid influx of microbes after birth, followed by dynamic shifts during the first few weeks of life. Microbial transplantation was found to reshape the genetic makeup of 33 metagenomic-assembled genomes (FDR < 0.05), mainly from Prevotella and Bacteroides species. We further linked over 20 million microbial single nucleotide variations to 736 plasma metabolites, which enabled us to characterize 24 study-wide significant associations (P < 4.4 × 10-9) that identify the potential microbial genetic regulation of host immune and neuro-related metabolites, including glutathione and L-dopa. Our integration analyses further revealed that microbial genetic variations may influence the health status and growth performance by modulating metabolites via structural regulation of their encoded proteins. For instance, we found that the albumin levels and total antioxidant capacity were correlated with L-dopa, which was determined by single nucleotide variations via structural regulations of metabolic enzymes. The current results indicate that temporal colonization and transplantation-driven strain replacement are crucial for newborn gut development, offering insights for enhancing newborn health and growth.
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Affiliation(s)
- Quanbin Dong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Dongxu Hua
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Xiuchao Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
| | - Yuwen Jiao
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
| | - Lu Liu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Qiufeng Deng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Tingting Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Huayiyang Zou
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Chen Zhao
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Chengkun Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Jiafa Reng
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Luoyang Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shixian Hu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Jing Shi
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Yifeng Wang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Haifeng Zhang
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Yanhui Sheng
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Wei Sun
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
| | - Yizhao Shen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Liming Tang
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
| | - Xiangqing Kong
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
- Cardiovascular Research Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215006, China
| | - Lianmin Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing 210029, China
- Changzhou Medical Center, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Nanjing Medical University, Changzhou 213164, China
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18
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Peoples LM, Dore JE, Bilbrey EM, Vick-Majors TJ, Ranieri JR, Evans KA, Ross AM, Devlin SP, Church MJ. Oxic methane production from methylphosphonate in a large oligotrophic lake: limitation by substrate and organic carbon supply. Appl Environ Microbiol 2023; 89:e0109723. [PMID: 38032216 PMCID: PMC10734540 DOI: 10.1128/aem.01097-23] [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: 06/28/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Methane is an important greenhouse gas that is typically produced under anoxic conditions. We show that methane is supersaturated in a large oligotrophic lake despite the presence of oxygen. Metagenomic sequencing indicates that diverse, widespread microorganisms may contribute to the oxic production of methane through the cleavage of methylphosphonate. We experimentally demonstrate that these organisms, especially members of the genus Acidovorax, can produce methane through this process. However, appreciable rates of methane production only occurred when both methylphosphonate and labile sources of carbon were added, indicating that this process may be limited to specific niches and may not be completely responsible for methane concentrations in Flathead Lake. This work adds to our understanding of methane dynamics by describing the organisms and the rates at which they can produce methane through an oxic pathway in a representative oligotrophic lake.
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Affiliation(s)
- Logan M. Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E. Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Evan M. Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Trista J. Vick-Majors
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - John R. Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A. Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Abigail M. Ross
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Shawn P. Devlin
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J. Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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Commichaux S, Luan T, Muralidharan HS, Pop M. Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571439. [PMID: 38168205 PMCID: PMC10760110 DOI: 10.1101/2023.12.13.571439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. The 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other marker genes as the number of gene sequences increases in reference databases. We demonstrate this effect through the analysis of three commonly used databases of nearly-universal prokaryotic marker genes: the SILVA 16S rRNA gene database, the Genome Taxonomy Database (GTDB), and a set of 40 taxonomically-informative single-copy genes. Our results reflect a more fundamental property of the taxonomies themselves and have broad implications for bioinformatic analyses beyond taxonomic classification. Effective solutions for fine-level taxonomic classification require a more precise, and operationally-relevant, definition of the taxonomic labels being sought, and the use of combinations of genomic markers in the classification process. Importance The use of reference databases for assigning taxonomic labels to genomic and metagenomic sequences is a fundamental bioinformatic task in the characterization of microbial communities. The increasing accessibility of high throughput sequencing has led to a rapid increase in the size and number of sequences in databases. This has been beneficial for improving our understanding of the global microbial genetic diversity. However, there is evidence that as the microbial diversity is more densely sampled, increasingly longer genomic segments are needed to differentiate between distinct species. The scientific community needs to be aware of this issue and needs to develop methods that better account for it when assigning taxonomic labels to metagenomic sequences from microbial communities.
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20
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Priest T, Vidal-Melgosa S, Hehemann JH, Amann R, Fuchs BM. Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic. ISME COMMUNICATIONS 2023; 3:130. [PMID: 38071398 PMCID: PMC10710508 DOI: 10.1038/s43705-023-00324-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 02/13/2024]
Abstract
Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and potential carbohydrate utilisation by microbes in Atlantic waters of the Arctic. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, while the more labile β-1,3-glucan exhibited a patchy distribution. Through 'omics analysis, we identify variations in the abundance and transcription of carbohydrate degradation-related genes across samples at the community and population level. The populations contributing the most to transcription were taxonomically related to those known as primary responders and key carbohydrate degraders in temperate ecosystems, such as NS4 Marine Group and Formosa. The unique transcription profiles for these populations suggest distinct substrate utilisation potentials, with predicted glycan targets corresponding to those structurally identified in POM from the same sampling sites. By combining cutting-edge technologies and protocols, we provide insights into the carbohydrate component of the carbon cycle in the Arctic during late summer and present a high-quality dataset that will be of great value for future comparative analyses.
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Affiliation(s)
- Taylor Priest
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, MARUM, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- University of Bremen, MARUM, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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21
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Konstantinidis KT. Sequence-discrete species for prokaryotes and other microbes: A historical perspective and pending issues. MLIFE 2023; 2:341-349. [PMID: 38818268 PMCID: PMC10989153 DOI: 10.1002/mlf2.12088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/04/2023] [Accepted: 10/08/2023] [Indexed: 06/01/2024]
Abstract
Whether prokaryotes, and other microorganisms, form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying, regulating, and communicating about these organisms. In the past decade, comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters, albeit organisms of intermediate relatedness between the identified clusters are also frequently found. Accumulating evidence suggests, however, that the latter "intermediate" organisms show enough ecological and/or functional distinctiveness to be considered different species. Notably, the area of discontinuity between clusters often-but not always-appears to be around 85%-95% genome-average nucleotide identity, consistently among different taxa. More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well. This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters. The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination, which mediates (successful) horizontal gene transfer, around 95% nucleotide identity. Deviations from the 95% threshold (e.g., species showing lower intraspecies diversity) may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer. While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency (i.e., higher recombination within vs. between groups) is appealing, the supporting evidence remains anecdotal. The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.
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Affiliation(s)
- Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological SciencesGeorgia Institute of TechnologyAtlantaGeorgiaUSA
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22
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Chiou YJ, Chan YF, Yu SP, Lu CY, Hsiao SSY, Chiang PW, Hsu TC, Liu PY, Wada N, Lee Y, Jane WN, Lee DC, Huang YW, Tang SL. Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas. SCIENCE ADVANCES 2023; 9:eadk1910. [PMID: 37992165 PMCID: PMC10664990 DOI: 10.1126/sciadv.adk1910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddD-harboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe.
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Affiliation(s)
- Yu-Jing Chiou
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ya-Fan Chan
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | | | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ting-Chang Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Der-Chuen Lee
- Institute of Astronomy and Astrophysics, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Wen Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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23
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Salamzade R, Kalan LR. skDER: microbial genome dereplication approaches for comparative and metagenomic applications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559801. [PMID: 38045253 PMCID: PMC10690176 DOI: 10.1101/2023.09.27.559801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
skDER ( https://github.com/raufs/skDER ) combines recent advances to efficiently estimate average nucleotide identity (ANI) between thousands of microbial genomes by skani 1 with two low-memory methods for genomic dereplication. The first method implements a dynamic algorithm to determine a concise set of representative genomes. This approach is well-suited for selecting reference genomes to align metagenomic reads onto for tracking strain presence across related microbiome samples. This is because fewer representative genomes should alleviate the concern that reads belonging to the same strain get falsely partitioned across closely related genomes. The other method, which uses a greedy approach, is better suited for use in comparative genomics, where users might be overwhelmed with the high number of genomes available for certain taxa and aim to reduce redundancy and, therefore, computational requirements for downstream analytics. This method selects a larger number of representative genomes to comprehensively sample the pangenome space for the taxon of interest. To further aid usage for comparative genomics studies, skDER also features an option to automatically download genomes classified as a particular species or genus in the Genome Taxonomy Database 2-4 and we provide precomputed representative genomes for commonly studied bacterial taxa 5 .
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Shaw J, Yu YW. Fast and robust metagenomic sequence comparison through sparse chaining with skani. Nat Methods 2023; 20:1661-1665. [PMID: 37735570 PMCID: PMC10630134 DOI: 10.1038/s41592-023-02018-3] [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: 02/07/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Sequence comparison tools for metagenome-assembled genomes (MAGs) struggle with high-volume or low-quality data. We present skani ( https://github.com/bluenote-1577/skani ), a method for determining average nucleotide identity (ANI) via sparse approximate alignments. skani outperforms FastANI in accuracy and speed (>20× faster) for fragmented, incomplete MAGs. skani can query genomes against >65,000 prokaryotic genomes in seconds and 6 GB memory. skani unlocks higher-resolution insights for extensive, noisy metagenomic datasets.
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Affiliation(s)
- Jim Shaw
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada.
| | - Yun William Yu
- Department of Mathematics, University of Toronto, Toronto, Ontario, Canada.
- Computer and Mathematical Sciences, University of Toronto at Scarborough, Toronto, Ontario, Canada.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
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25
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Chávez-Hernández M, Ortiz-Álvarez J, Morales-Jiménez J, Villa-Tanaca L, Hernández-Rodríguez C. Phenotypic and Genomic Characterization of Streptomyces pakalii sp. nov., a Novel Species with Anti-Biofilm and Anti-Quorum Sensing Activity in ESKAPE Bacteria. Microorganisms 2023; 11:2551. [PMID: 37894209 PMCID: PMC10608816 DOI: 10.3390/microorganisms11102551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The increasing number of infections caused by antimicrobial multi-resistant microorganisms has led to the search for new microorganisms capable of producing novel antibiotics. This work proposes Streptomyces pakalii sp. nov. as a new member of the Streptomycetaceae family. The strain ENCB-J15 was isolated from the jungle soil in Palenque National Park, Chiapas, Mexico. The strain formed pale brown, dry, tough, and buried colonies in the agar with no diffusible pigment in GAE (glucose-asparagine-yeast extract) medium. Scanning electron micrographs showed typical mycelium with long chains of smooth and oval-shaped spores (3-10 m). The strain grew in all of the International Streptomyces Project (ISP)'s media at 28-37 °C with a pH of 6-9 and 0-10% NaCl. S. pakalii ENCB-J15 assimilated diverse carbon as well as organic and inorganic nitrogen sources. The strain also exhibited significant inhibitory activity against the prodigiosin synthesis of Serratia marcescens and the inhibition of the formation and destruction of biofilms of ESKAPE strains of Acinetobacter baumannii and Klebsiella pneumoniae. The draft genome sequencing of ENCB-J15 revealed a 7.6 Mb genome with a high G + C content (71.6%), 6833 total genes, and 6746 genes encoding putative proteins. A total of 26 accessory clusters of proteins associated with carbon sources and amino acid catabolism, DNA modification, and the antibiotic biosynthetic process were annotated. The 16S rRNA gene phylogeny, core-proteome phylogenomic tree, and virtual genome fingerprints support that S. pakalii ENCB-J15 is a new species related to Streptomyces badius and Streptomyces globisporus. Similarly, its average nucleotide identity (ANI) (96.4%), average amino acid identity (AAI) (96.06%), and virtual DNA-DNA hybridization (67.3%) provide evidence to recognize it as a new species. Comparative genomics revealed that S. pakalli and its closest related species maintain a well-conserved genomic synteny. This work proposes Streptomyces pakalii sp. nov. as a novel species that expresses anti-biofilm and anti-quorum sensing activities.
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Affiliation(s)
- Michelle Chávez-Hernández
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - Jossue Ortiz-Álvarez
- Programa “Investigadoras e Investigadores por México”. Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT). Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México 03940, Mexico;
| | - Jesús Morales-Jiménez
- Departamento el Hombre y su Ambiente, Universidad Autónoma Metropolitana-Xochimilco, Calzada del Hueso 1100, Villa Quietud, Coyoacán, Ciudad de México 04960, Mexico;
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio y Plan de Ayala, Col. Sto. Tomás s/n, Ciudad de México 11340, Mexico; (M.C.-H.); (L.V.-T.)
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26
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Kobayashi Y, Kayamori A, Aoki K, Shiwa Y, Matsutani M, Fujita N, Sugita T, Iwasaki W, Tanaka N, Takashima M. Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny. BMC Genomics 2023; 24:609. [PMID: 37821828 PMCID: PMC10568926 DOI: 10.1186/s12864-023-09718-2] [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: 06/15/2023] [Accepted: 10/05/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Since DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity. RESULTS The long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces. CONCLUSIONS Our results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.
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Affiliation(s)
- Yuuki Kobayashi
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
| | - Ayane Kayamori
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Keita Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Minenosuke Matsutani
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Nobuyuki Fujita
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Takashi Sugita
- Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo, 204-8588, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Naoto Tanaka
- Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Masako Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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Reyes-Umana VM, Coates JD. A description of the genus Denitromonas nom. rev.: Denitromonas iodatirespirans sp. nov., a novel iodate-reducing bacterium, and two novel perchlorate-reducing bacteria, Denitromonas halophila and Denitromonas ohlonensis, isolated from San Francisco Bay intertidal mudflats. Microbiol Spectr 2023; 11:e0091523. [PMID: 37772843 PMCID: PMC10581121 DOI: 10.1128/spectrum.00915-23] [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: 03/03/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
The genus Denitromonas is currently a non-validated taxon that has been identified in several recent publications as members of microbial communities arising from marine environments. Very little is known about the biology of Denitromonas spp., and no pure cultures are presently found in any culture collections. The current epitaph of Denitromonas was given to the organism under the assumption that all members of this genus are denitrifying bacteria. This study performs phenotypic and genomic analyses on three new Denitromonas spp. isolated from tidal mudflats in the San Francisco Bay. We demonstrate that Denitromonas spp. are indeed all facultative denitrifying bacteria that utilize a variety of carbon sources such as acetate, lactate, and succinate. In addition, individual strains also use the esoteric electron acceptors perchlorate, chlorate, and iodate. Both 16S and Rps/Rpl phylogenetic analyses place Denitromonas spp. as a deep branching clade in the family Zoogloeaceae, separate from either Thauera spp., Azoarcus spp., or Aromatoleum spp. Genome sequencing reveals a G + C content ranging from 63.72% to 66.54%, and genome sizes range between 4.39 and 5.18 Mb. Genes for salt tolerance and denitrification are distinguishing features that separate Denitromonas spp. from the closely related Azoarcus and Aromatoleum genera. IMPORTANCE The genus Denitromonas is currently a non-validated taxon that has been identified in several recent publications as members of microbial communities arising from marine environments. Very little is known about the biology of Denitromonas spp., and no pure cultures are presently found in any culture collections. The current epitaph of Denitromonas was given to the organism under the assumption that all members of this genus are denitrifying bacteria. This study performs phenotypic and genomic analyses on three Denitromonas spp., Denitromonas iodatirespirans sp. nov.-a novel iodate-reducing bacterium-and two novel perchlorate-reducing bacteria, Denitromonas halophila and Denitromonas ohlonensis, isolated from San Francisco Bay intertidal mudflats.
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Affiliation(s)
- Victor M. Reyes-Umana
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - John D. Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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28
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Cobo-Simón M, Hart R, Ochman H. Gene flow and species boundaries of the genus Salmonella. mSystems 2023; 8:e0029223. [PMID: 37486130 PMCID: PMC10470047 DOI: 10.1128/msystems.00292-23] [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: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 07/25/2023] Open
Abstract
The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica, which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6-10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis-i.e., subsp. enterica and diarizonae-were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella, that demonstrate complex patterns of species and subspecies divergence. IMPORTANCE The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella, whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori, several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.
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Affiliation(s)
- Marta Cobo-Simón
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Rowan Hart
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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29
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Liao J, Shenhav L, Urban JA, Serrano M, Zhu B, Buck GA, Korem T. Microdiversity of the vaginal microbiome is associated with preterm birth. Nat Commun 2023; 14:4997. [PMID: 37591872 PMCID: PMC10435516 DOI: 10.1038/s41467-023-40719-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.
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Affiliation(s)
- Jingqiu Liao
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA.
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
| | - Julia A Urban
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Myrna Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Bin Zhu
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, ON, Canada.
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30
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Salamzade R, Tran P, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544063. [PMID: 37333121 PMCID: PMC10274777 DOI: 10.1101/2023.06.07.544063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous or homologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of protein-encoding ortholog groups for individual genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of statistics for each inferred ortholog group. These programs are showcased through application to: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-genetic insights of two common BGCs in a fungal species, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Science Doctoral Program, University of Wisconsin-Madison, WI, USA
| | - Cody Martin
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Gilmore
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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31
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Jespersen ML, Munk P, Johansen J, Kaas RS, Webel H, Vigre H, Nielsen HB, Rasmussen S, Aarestrup FM. Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering. Commun Biol 2023; 6:700. [PMID: 37422584 PMCID: PMC10329687 DOI: 10.1038/s42003-023-05083-8] [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: 06/01/2022] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
Most investigations of geographical within-species differences are limited to focusing on a single species. Here, we investigate global differences for multiple bacterial species using a dataset of 757 metagenomics sewage samples from 101 countries worldwide. The within-species variations were determined by performing genome reconstructions, and the analyses were expanded by gene focused approaches. Applying these methods, we recovered 3353 near complete (NC) metagenome assembled genomes (MAGs) encompassing 1439 different MAG species and found that within-species genomic variation was in 36% of the investigated species (12/33) coherent with regional separation. Additionally, we found that variation of organelle genes correlated less with geography compared to metabolic and membrane genes, suggesting that the global differences of these species are caused by regional environmental selection rather than dissemination limitations. From the combination of the large and globally distributed dataset and in-depth analysis, we present a wide investigation of global within-species phylogeny of sewage bacteria. The global differences found here emphasize the need for worldwide data sets when making global conclusions.
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Affiliation(s)
- Marie Louise Jespersen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Rolf Sommer Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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32
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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33
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Grenfell AW, Intile PJ, McFarlane JA, Leung DC, Abdalla K, Wold MC, Kees ED, Gralnick JA. The Outer Membrane Cytochrome OmcA Is Essential for Infection of Shewanella oneidensis by a Zebrafish-Associated Bacteriophage. J Bacteriol 2023; 205:e0046922. [PMID: 37227287 PMCID: PMC10294696 DOI: 10.1128/jb.00469-22] [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: 12/07/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
The microbiota-the mixture of microorganisms in the intestinal tract of animals-plays an important role in host biology. Bacteriophages are a prominent, though often overlooked, component of the microbiota. The mechanisms that phage use to infect susceptible cells associated with animal hosts, and the broader role they could play in determining the substituents of the microbiota, are poorly understood. In this study, we isolated a zebrafish-associated bacteriophage, which we named Shewanella phage FishSpeaker. This phage infects Shewanella oneidensis strain MR-1, which cannot colonize zebrafish, but it is unable to infect Shewanella xiamenensis strain FH-1, a strain isolated from the zebrafish gut. Our data suggest that FishSpeaker uses the outer membrane decaheme cytochrome OmcA, which is an accessory component of the extracellular electron transfer (EET) pathway in S. oneidensis, as well as the flagellum to recognize and infect susceptible cells. In a zebrafish colony that lacks detectable FishSpeaker, we found that most Shewanella spp. are sensitive to infection and that some strains are resistant to infection. Our results suggest that phage could act as a selectivity filter for zebrafish-associated Shewanella and show that the EET machinery can be targeted by phage in the environment. IMPORTANCE Phage exert selective pressure on bacteria that influences and shapes the composition of microbial populations. However, there is a lack of native, experimentally tractable systems for studying how phage influence microbial population dynamics in complex communities. Here, we show that a zebrafish-associated phage requires both the outer membrane-associated extracellular electron transfer protein OmcA and the flagellum to infect Shewanella oneidensis strain MR-1. Our results suggest that the newly discovered phage-FishSpeaker-could exert selective pressure that restricts which Shewanella spp. colonize zebrafish. Moreover, the requirement of OmcA for infection by FishSpeaker suggests that the phage preferentially infects cells that are oxygen limited, a condition required for OmcA expression and an ecological feature of the zebrafish gut.
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Affiliation(s)
- Andrew W. Grenfell
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Peter J. Intile
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - John A. McFarlane
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Dani C. Leung
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Khalid Abdalla
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Michael C. Wold
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Eric D. Kees
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
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34
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Liao J, Shenhav L, Urban JA, Serrano M, Zhu B, Buck GA, Korem T. Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523991. [PMID: 36711990 PMCID: PMC9882146 DOI: 10.1101/2023.01.13.523991] [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: 06/09/2023]
Abstract
Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield new insights into these associations. To this end, we analyzed metagenomic data from 705 vaginal samples collected longitudinally during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI). We find that the vaginal microbiome of pregnancies that ended preterm exhibits unique genetic profiles. It is more genetically diverse at the species level, a result which we validate in an additional cohort, and harbors a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species, a group of central vaginal pathobionts, are driving this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. undergoes more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our results reveal novel associations between the vaginal microbiome and PTB using population genetics analyses, and suggest that evolutionary processes acting on the vaginal microbiome may play a vital role in adverse pregnancy outcomes such as preterm birth.
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Affiliation(s)
- Jingqiu Liao
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
| | - Julia A. Urban
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Myrna Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Bin Zhu
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A. Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada
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35
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Hochart C, Paoli L, Ruscheweyh HJ, Salazar G, Boissin E, Romac S, Poulain J, Bourdin G, Iwankow G, Moulin C, Ziegler M, Porro B, Armstrong EJ, Hume BCC, Aury JM, Pogoreutz C, Paz-García DA, Nugues MM, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Gilson E, Lombard F, Pesant S, Reynaud S, Thomas OP, Troublé R, Wincker P, Zoccola D, Allemand D, Planes S, Thurber RV, Voolstra CR, Sunagawa S, Galand PE. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nat Commun 2023; 14:3037. [PMID: 37264015 DOI: 10.1038/s41467-023-38502-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/26/2023] [Indexed: 06/03/2023] Open
Abstract
Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.
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Affiliation(s)
- Corentin Hochart
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | | | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 (IFZ), 35392, Giessen, Germany
| | - Barbara Porro
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric J Armstrong
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Benjamin C C Hume
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Claudia Pogoreutz
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maggy M Nugues
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, 04469, USA
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Paola Furla
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
| | - Eric Gilson
- CNRS, INSERM, Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Department of Medical Genetics, CHU Nice, Nice, France
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
- Institut Universitaire de France, 75231, Paris, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, 8 rue de Prague, 75012, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | - Didier Zoccola
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Denis Allemand
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco (LIA ROPSE), Monaco, Principality of Monaco
- Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
| | | | | | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093, Zürich, Switzerland
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur Mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
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Schwartz DJ, Shalon N, Wardenburg K, DeVeaux A, Wallace MA, Hall-Moore C, Ndao IM, Sullivan JE, Radmacher P, Escobedo M, D. Burnham CA, Warner BB, Tarr PI, Dantas G. Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Sci Transl Med 2023; 15:eadg5562. [PMID: 37134153 PMCID: PMC10259202 DOI: 10.1126/scitranslmed.adg5562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023]
Abstract
Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.
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Affiliation(s)
- Drew J. Schwartz
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nitan Shalon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kate Wardenburg
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anna DeVeaux
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carla Hall-Moore
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I. Malick Ndao
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janice E. Sullivan
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children’s Hospital, Louisville, KY 40202, USA
| | - Paula Radmacher
- Department of Pediatrics, University of Louisville School of Medicine, Norton Children’s Hospital, Louisville, KY 40202, USA
| | - Marilyn Escobedo
- Department of Pediatrics, University of Oklahoma, Oklahoma City, OK 73117, USA
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Barbara B. Warner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Phillip I. Tarr
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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37
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De León ME, Wilson HS, Jospin G, Eisen JA. Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives. Microb Genom 2023; 9. [PMID: 37052581 PMCID: PMC10210950 DOI: 10.1099/mgen.0.000971] [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: 09/10/2022] [Accepted: 01/31/2023] [Indexed: 04/14/2023] Open
Abstract
Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein have been isolated from diverse environments including fresh and ocean waters, glaciers, tropical soils, trees, fish and the skin of amphibians. We report here the isolation and characterization of six violacein-producing bacterial strains and three non-violacein-producing close relatives, each isolated from either an aquatic environment or moist food materials in northern California, USA. For each isolate, we characterized traditional phenotypes, generated and analysed draft genome sequences, and carried out multiple types of taxonomic, phylogenetic and phylogenomic analyses. Based on these analyses we assign putative identifications to the nine isolates, which include representatives of the genera Chromobacterium, Aquitalea, Iodobacter, Duganella, Massilia and Janthinobacterium. In addition, we discuss the utility of various metrics for taxonomic assignment in these groups including average nucleotide identity, whole genome phylogenetic analysis and extent of recent homologous recombination using the software program PopCOGenT.
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Affiliation(s)
| | - Harriet S Wilson
- Department of Biological Sciences, Sierra College, Rocklin, CA, USA
| | - Guillaume Jospin
- Genome Center, University of California, Davis, CA, USA
- AnimalBiome, Oakland, CA, USA
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
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38
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Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression. THE ISME JOURNAL 2023; 17:813-822. [PMID: 36871069 DOI: 10.1038/s41396-023-01390-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023]
Abstract
Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species' divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species' pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.
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Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot. THE ISME JOURNAL 2023; 17:354-370. [PMID: 36536072 PMCID: PMC9938248 DOI: 10.1038/s41396-022-01345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.
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40
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Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, Xiao X, Li J, Jia K, Greening C, Shao Z, Hubert CRJ. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun 2023; 14:1127. [PMID: 36854684 PMCID: PMC9974965 DOI: 10.1038/s41467-023-36877-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Muhua Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Laura Woods
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Wenxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510075, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Zhao C, Shi ZJ, Pollard KS. Pitfalls of genotyping microbial communities with rapidly growing genome collections. Cell Syst 2023; 14:160-176.e3. [PMID: 36657438 PMCID: PMC9957970 DOI: 10.1016/j.cels.2022.12.007] [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: 06/30/2022] [Revised: 10/15/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023]
Abstract
Detecting genetic variants in metagenomic data is a priority for understanding the evolution, ecology, and functional characteristics of microbial communities. Many tools that perform this metagenotyping rely on aligning reads of unknown origin to a database of sequences from many species before calling variants. In this synthesis, we investigate how databases of increasingly diverse and closely related species have pushed the limits of current alignment algorithms, thereby degrading the performance of metagenotyping tools. We identify multi-mapping reads as a prevalent source of errors and illustrate a trade-off between retaining correct alignments versus limiting incorrect alignments, many of which map reads to the wrong species. Then we evaluate several actionable mitigation strategies and review emerging methods showing promise to further improve metagenotyping in response to the rapid growth in genome collections. Our results have implications beyond metagenotyping to the many tools in microbial genomics that depend upon accurate read mapping.
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Affiliation(s)
- Chunyu Zhao
- Chan Zuckerberg Biohub, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Zhou Jason Shi
- Chan Zuckerberg Biohub, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Katherine S Pollard
- Chan Zuckerberg Biohub, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
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42
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Site Specialization of Human Oral Veillonella Species. Microbiol Spectr 2023; 11:e0404222. [PMID: 36695592 PMCID: PMC9927086 DOI: 10.1128/spectrum.04042-22] [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] [Indexed: 01/26/2023] Open
Abstract
Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.
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Salamzade R, Swaney MH, Kalan LR. Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease. Microbiol Spectr 2023; 11:e0357822. [PMID: 36541755 PMCID: PMC9927478 DOI: 10.1128/spectrum.03578-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Corynebacterium are a diverse genus and dominant member of the human skin microbiome. Recently, we reported that the most prevalent Corynebacterium species found on skin, including Corynebacterium tuberculostearicum and Corynebacterium kefirresidentii, comprise a narrow species complex despite the diversity of the genus. Here, we apply high-resolution phylogenomics and comparative genomics to describe the structure of the C. tuberculostearicum species complex and highlight genetic traits which are enriched or depleted in it relative to other Corynebacterium. Through metagenomic investigations, we also find that individual species within the complex can associate with specific body sites. Finally, we discover that one species from the complex, C. kefirresidentii, increases in relative abundance during atopic dermatitis flares, and show that most genomes of this species encode a colocalized set of putative virulence genes. IMPORTANCE Corynebacterium are commonly found bacteria on the human skin. In this study, we perform comparative genomics to gain insight into genetic traits which differentiate a phylogenetically related group of Corynebacterium, the Corynebacterium tuberculostearicum species complex, that includes the most prevalent species from the genus in skin microbiomes. After resolving the presence of distinct species within the complex, we applied metagenomic analysis to uncover biogeographic associations of individual species within the complex with specific body sites and discovered that one species, commonly found in the nares of individuals, increases in abundance across multiple body sites during atopic dermatitis flares.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, Wisconsin, USA
| | - Mary Hannah Swaney
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, Wisconsin, USA
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Dong X, Lan H, Huang L, Zhang H, Lin X, Weng S, Peng Y, Lin J, Wang JH, Peng J, Yang Y. Metagenomic Views of Microbial Communities in Sand Sediments Associated with Coral Reefs. MICROBIAL ECOLOGY 2023; 85:465-477. [PMID: 35113183 DOI: 10.1007/s00248-021-01957-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Reef sediments, the home for microbes with high abundances, provide an important source of carbonates and nutrients for the growth and maintenance of coral reefs. However, there is a lack of systematic research on the composition of microbial community in sediments of different geographic sites and their potential effect on nutrient recycling and health of the coral reef ecosystem. In combination of biogeochemical measurements with gene- and genome-centric metagenomics, we assessed microbial community compositions and functional diversity, as well as profiles of antibiotic resistance genes in surface sediments of 16 coral reef sites at different depths from the Xisha islands in the South China Sea. Reef sediment microbiomes are diverse and novel at lower taxonomic ranks, dominated by Proteobacteria and Planctomycetota. Most reef sediment bacteria potentially participate in biogeochemical cycling via oxidizing various organic and inorganic compounds as energy sources. High abundances of Proteobacteria (mostly Rhizobiales and Woeseiales) are metabolically flexible and contain rhodopsin genes. Various classes of antibiotic resistance genes, hosted by diverse bacterial lineages, were identified to confer resistance to multidrug, aminoglycoside, and other antibiotics. Overall, our findings expanded the understanding of reef sediment microbial ecology and provided insights for their link to the coral reef ecosystem health.
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Affiliation(s)
- Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Haoyu Lan
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Liangtian Huang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Haikun Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xianbiao Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jia Lin
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Juan Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Ying Yang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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45
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Rai A, Suresh G, Ria B, L V, Pk S, Ipsita S, Sasikala C, Venkata Ramana C. Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748586 DOI: 10.1099/ijsem.0.005672] [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: 01/12/2023] Open
Abstract
The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.
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Affiliation(s)
- Anusha Rai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Biswas Ria
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Vighnesh L
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sreya Pk
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sahu Ipsita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad-500 085, India
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
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46
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Cryptic Diversity of Black Band Disease Cyanobacteria in Siderastrea siderea Corals Revealed by Chemical Ecology and Comparative Genome-Resolved Metagenomics. Mar Drugs 2023; 21:md21020076. [PMID: 36827117 PMCID: PMC9967302 DOI: 10.3390/md21020076] [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: 12/09/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Black band disease is a globally distributed and easily recognizable coral disease. Despite years of study, the etiology of this coral disease, which impacts dozens of stony coral species, is not completely understood. Although black band disease mats are predominantly composed of the cyanobacterial species Roseofilum reptotaenium, other filamentous cyanobacterial strains and bacterial heterotrophs are readily detected. Through chemical ecology and metagenomic sequencing, we uncovered cryptic strains of Roseofilum species from Siderastrea siderea corals that differ from those on other corals in the Caribbean and Pacific. Isolation of metabolites from Siderastrea-derived Roseofilum revealed the prevalence of unique forms of looekeyolides, distinct from previously characterized Roseofilum reptotaenium strains. In addition, comparative genomics of Roseofilum strains showed that only Siderastrea-based Roseofilum strains have the genetic capacity to produce lasso peptides, a family of compounds with diverse biological activity. All nine Roseofilum strains examined here shared the genetic capacity to produce looekeyolides and malyngamides, suggesting these compounds support the ecology of this genus. Similar biosynthetic gene clusters are not found in other cyanobacterial genera associated with black band disease, which may suggest that looekeyolides and malyngamides contribute to disease etiology through yet unknown mechanisms.
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Shi LD, Gao TY, Wei XW, Shapleigh JP, Zhao HP. pH-Dependent Hydrogenotrophic Denitratation Based on Self-Alkalization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:685-696. [PMID: 36408861 DOI: 10.1021/acs.est.2c05559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Producing stable nitrite is a necessity for anaerobic ammonium oxidation (anammox) but remains a huge challenge. Here, we describe the design and operation of a hydrogenotrophic denitratation system that stably reduced >90% nitrate to nitrite under self-alkaline conditions of pH up to 10.80. Manually lowering the pH to a range of 9.00-10.00 dramatically decreased the nitrate-to-nitrite transformation ratio to <20%, showing a significant role of high pH in denitratation. Metagenomics combined with metatranscriptomics indicated that six microorganisms, including a Thauera member, dominated the community and encoded the various genes responsible for hydrogen oxidation and the complete denitrification process. During denitratation at high pH, transcription of periplasmic genes napA, nirS, and nirK, whose products perform nitrate and nitrite reduction, decreased sharply compared to that under neutral conditions, while narG, encoding a membrane-associated nitrate reductase, remained transcriptionally active, as were genes involved in intracellular proton homeostasis. Together with no reduction in only nitrite-amended samples, these results disproved the electron competition between reductions of nitrate and nitrite but highlighted a lack of protons outside cells constraining biological nitrite reduction. Overall, our study presents a stably efficient strategy for nitrite production and provides a major advance in the understanding of denitratation.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - Tian-Yu Gao
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - Xiao-Wen Wei
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, New York14853, United States
| | - He-Ping Zhao
- MOE Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou310058, Zhejiang, China
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Xiang B, Zhao L, Zhang M. Unitig level assembly graph based metagenome-assembled genome refiner (UGMAGrefiner): A tool to increase completeness and resolution of metagenome-assembled genomes. Comput Struct Biotechnol J 2023; 21:2394-2404. [PMID: 37066122 PMCID: PMC10091015 DOI: 10.1016/j.csbj.2023.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 04/03/2023] Open
Abstract
De novo assembly of next generation metagenomic reads is widely used to provide taxonomic and functional information of genomes in a microbial community. As strains are functionally specific, recovery of strain-resolved genomes is important but still a challenge. Unitigs and assembly graphs are mid-products generated during the assembly of reads into contigs, and they provide higher resolution for sequences connection information. In this study, we propose a new approach UGMAGrefiner (a unitig level assembly graph-based metagenome-assembled Genome refiner), which uses the connection and coverage information from unitig level assembly graphs to recruit unbinned unitigs to MAGs, adjust binning result, and infer unitigs shared by multiple MAGs. In two simulated datasets (Simdata and CAMI data) and one real dataset (GD02), it outperforms two state-of-the-art assembly graph-based binning refine tools in the refinement of MAGs' quality by stably increasing the completeness of genomes. UGMAGrefiner can identify genome specific clusters of genomes with below 99% average nucleotide identity for homologous sequences. For MAGs mixed with 99% similarity genome clusters, it could distinguish 8 out of 9 genomes in Simdata and 8 out of 12 genomes in CAMI data. In GD02 data, it could identify 16 new unitig clusters representing genome specific regions of mixed genomes and 4 unitig clusters representing new genomes from total 135 MAGs for further functional analysis. UGMAGrefiner provides an efficient way to obtain more complete MAGs and study genome specific functions. It will be useful to improve taxonomic and functional information of genomes after de novo assembly.
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McLean AR, Torres-Morales J, Dewhirst FE, Borisy GG, Welch JLM. Site-tropism of streptococci in the oral microbiome. Mol Oral Microbiol 2022; 37:229-243. [PMID: 36073311 PMCID: PMC9691528 DOI: 10.1111/omi.12387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/08/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022]
Abstract
A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.
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Affiliation(s)
- Anthony R. McLean
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
| | | | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, MA 02142
- Harvard School of Dental Medicine, Boston, MA 02115
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
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Perez-Fernandez CA, Wilburn P, Davila A, DiRuggiero J. Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert. Sci Rep 2022; 12:20022. [PMID: 36414646 PMCID: PMC9681764 DOI: 10.1038/s41598-022-23437-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
The adaptation mechanisms of microbial communities to natural perturbations remain unexplored, particularly in extreme environments. The extremophilic communities of halite (NaCl) nodules from the hyper-arid core of the Atacama Desert are self-sustained and represent a unique opportunity to study functional adaptations and community dynamics with changing environmental conditions. We transplanted halite nodules to different sites in the desert and investigated how their taxonomic, cellular, and biochemical changes correlated with water availability, using environmental data modeling and metagenomic analyses. Salt-in strategists, mainly represented by haloarchaea, significantly increased in relative abundance at sites characterized by extreme dryness, multiple wet/dry cycles, and colder conditions. The functional analysis of metagenome-assembled genomes (MAGs) revealed site-specific enrichments in archaeal MAGs encoding for the uptake of various compatible solutes and for glycerol utilization. These findings suggest that opportunistic salt-in strategists took over the halite communities at the driest sites. They most likely benefited from compounds newly released in the environment by the death of microorganisms least adapted to the new conditions. The observed changes were consistent with the need to maximize cellular bioenergetics when confronted with lower water availability and higher salinity, providing valuable information on microbial community adaptations and resilience to climate change.
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Affiliation(s)
- Cesar A. Perez-Fernandez
- grid.21107.350000 0001 2171 9311Department of Biology, The Johns Hopkins University, Baltimore, MD USA
| | - Paul Wilburn
- grid.419075.e0000 0001 1955 7990NASA Ames Research Center-Exobiology Branch MS 239-4, Moffett Field, CA USA
| | - Alfonso Davila
- grid.419075.e0000 0001 1955 7990NASA Ames Research Center-Exobiology Branch MS 239-4, Moffett Field, CA USA
| | - Jocelyne DiRuggiero
- grid.21107.350000 0001 2171 9311Department of Biology, The Johns Hopkins University, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Earth and Planetary Sciences, The Johns Hopkins University, Baltimore, MD USA
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