1
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Gao SM, Wang P, Li Q, Shu WS, Tang LY, Lin ZL, Li JT, Huang LN. Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135478. [PMID: 39137550 DOI: 10.1016/j.jhazmat.2024.135478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/28/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Pandeng Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Ling-Yun Tang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
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2
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Baquero DP, Medvedeva S, Martin-Gallausiaux C, Pende N, Sartori-Rupp A, Tachon S, Pedron T, Debarbieux L, Borrel G, Gribaldo S, Krupovic M. Stable coexistence between an archaeal virus and the dominant methanogen of the human gut. Nat Commun 2024; 15:7702. [PMID: 39231967 PMCID: PMC11375127 DOI: 10.1038/s41467-024-51946-x] [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: 04/18/2024] [Accepted: 08/21/2024] [Indexed: 09/06/2024] Open
Abstract
The human gut virome, which is mainly composed of bacteriophages, also includes viruses infecting archaea, yet their role remains poorly understood due to lack of isolates. Here, we characterize a temperate archaeal virus (MSTV1) infecting Methanobrevibacter smithii, the dominant methanogenic archaeon of the human gut. The MSTV1 genome is integrated in the host chromosome as a provirus which is sporadically induced, resulting in virion release. Using cryo-electron tomography, we capture several intracellular virion assembly intermediates and confirm that only a small fraction of the host population actively produces virions in vitro. Similar low frequency of induction is observed in a mouse colonization model, using mice harboring a stable consortium of 12 bacterial species (OMM12). Transcriptomic analysis suggests a regulatory lysogeny-lysis switch involving an interplay between viral proteins to maintain virus-host equilibrium, ensuring host survival and viral persistence. Thus, our study sheds light on archaeal virus-host interactions and highlights similarities with bacteriophages in establishing stable coexistence with their hosts in the gut.
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Affiliation(s)
- Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Camille Martin-Gallausiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Nika Pende
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
- University of Vienna, Archaea Physiology and Biotechnology Group, Vienna, Austria
| | - Anna Sartori-Rupp
- Institut Pasteur, NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Stéphane Tachon
- Institut Pasteur, NanoImaging Core Facility, Centre de Ressources et Recherches Technologiques (C2RT), Paris, France
| | - Thierry Pedron
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
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3
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Flamholz ZN, Li C, Kelly L. Improving viral annotation with artificial intelligence. mBio 2024:e0320623. [PMID: 39230289 DOI: 10.1128/mbio.03206-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024] Open
Abstract
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environmental pressures. High-throughput sequencing approaches have begun to give us access to the diversity and range of phage populations in complex microbial community samples, and metagenomics is currently the primary tool with which we study phage populations. The study of phages by metagenomic sequencing, however, is fundamentally limited by viral diversity, which results in the vast majority of viral genomes and metagenome-annotated genomes lacking annotation. To harness bacteriophages for applications in human and environmental health and disease, we need new methods to organize and annotate viral sequence diversity. We recently demonstrated that methods that leverage self-supervised representation learning can supplement statistical sequence representations for remote viral protein homology detection in the ocean virome and propose that consideration of the functional content of viral sequences allows for the identification of similarity in otherwise sequence-diverse viruses and viral-like elements for biological discovery. In this review, we describe the potential and pitfalls of large language models for viral annotation. We describe the need for new approaches to annotate viral sequences in metagenomes, the fundamentals of what protein language models are and how one can use them for sequence annotation, the strengths and weaknesses of these models, and future directions toward developing better models for viral annotation more broadly.
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Affiliation(s)
- Zachary N Flamholz
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Charlotte Li
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
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4
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Mi J, Jing X, Ma C, Yang Y, Li Y, Zhang Y, Long R, Zheng H. Massive expansion of the pig gut virome based on global metagenomic mining. NPJ Biofilms Microbiomes 2024; 10:76. [PMID: 39209853 PMCID: PMC11362615 DOI: 10.1038/s41522-024-00554-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.
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Affiliation(s)
- Jiandui Mi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou, China.
| | - Xiaoping Jing
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, China
| | | | - Yiwen Yang
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yong Li
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yu Zhang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Ruijun Long
- State Key Laboratory of Grassland and Agro-Ecosystems, International Centre for Tibetan Plateau Ecosystem Management, College of Ecology, Lanzhou University, Lanzhou, China.
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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5
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Crouch AL, Monsey L, Rambeau M, Ramos C, Yracheta JM, Anderson MZ. Metagenomic discovery of microbial eukaryotes in stool microbiomes. mBio 2024:e0206324. [PMID: 39207108 DOI: 10.1128/mbio.02063-24] [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: 07/15/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.
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Affiliation(s)
- Audra L Crouch
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Laine Monsey
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Molly Rambeau
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Cameron Ramos
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Center for Genomic Science Innovation, University of Wisconsin - Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, Wisconsin, USA
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6
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Yang N, Ma T, Xie Y, Li Q, Li Y, Zheng L, Li Y, Xiao Q, Sun Z, Zuo K, Kwok LY, Lu N, Liu W, Zhang H. Lactiplantibacillus plantarum P9 for chronic diarrhea in young adults: a large double-blind, randomized, placebo-controlled trial. Nat Commun 2024; 15:6823. [PMID: 39122704 PMCID: PMC11315937 DOI: 10.1038/s41467-024-51094-2] [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: 05/10/2023] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Current treatments for chronic diarrhea have limited efficacy and several side effects. Probiotics have the potential to alleviate symptoms of diarrhea. This randomized, double-blind, placebo-controlled trial evaluates the effects of administering the probiotic Lactiplantibacillus plantarum P9 (P9) strain in young adults with chronic diarrhea (Clinical Trial Registration Number: ChiCTR2000038410). The intervention period lasts for 28 days, followed by a 14-day post-intervention period. Participants are randomized into the P9 (n = 93) and placebo (n = 96) groups, with 170 individuals completing the double-blind intervention phase (n = 85 per group). The primary endpoint is the diarrhea symptom severity score. Both intention-to-treat (n = 189) and per-protocol (n = 170) analyses reveal a modest yet statistically significant reduction in diarrhea severity compared to the placebo group (20.0%, P = 0.050; 21.4%, P = 0.048, respectively). In conclusion, the results of this study support the use of probiotics in managing chronic diarrhea in young adults. However, the lack of blood parameter assessment and the short intervention period represent limitations of this study.
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Affiliation(s)
- Ni Yang
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Teng Ma
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yong Xie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qiong Li
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yingmeng Li
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Longjin Zheng
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Yalin Li
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Qiuping Xiao
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Zhihong Sun
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Kexuan Zuo
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Nonghua Lu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Wenjun Liu
- State Key Laboratory for the Modernization of Classical and Famous Prescriptions of Chinese Medicine, Nanchang, China.
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, China.
| | - Heping Zhang
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
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7
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Howard A, Carroll-Portillo A, Alcock J, Lin HC. Dietary Effects on the Gut Phageome. Int J Mol Sci 2024; 25:8690. [PMID: 39201374 PMCID: PMC11354428 DOI: 10.3390/ijms25168690] [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: 06/20/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
As knowledge of the gut microbiome has expanded our understanding of the symbiotic and dysbiotic relationships between the human host and its microbial constituents, the influence of gastrointestinal (GI) microbes both locally and beyond the intestine has become evident. Shifts in bacterial populations have now been associated with several conditions including Crohn's disease (CD), Ulcerative Colitis (UC), irritable bowel syndrome (IBS), Alzheimer's disease, Parkinson's Disease, liver diseases, obesity, metabolic syndrome, anxiety, depression, and cancers. As the bacteria in our gut thrive on the food we eat, diet plays a critical role in the functional aspects of our gut microbiome, influencing not only health but also the development of disease. While the bacterial microbiome in the context of disease is well studied, the associated gut phageome-bacteriophages living amongst and within our bacterial microbiome-is less well understood. With growing evidence that fluctuations in the phageome also correlate with dysbiosis, how diet influences this population needs to be better understood. This review surveys the current understanding of the effects of diet on the gut phageome.
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Affiliation(s)
- Andrea Howard
- School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Amanda Carroll-Portillo
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Joe Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Henry C. Lin
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM 87131, USA
- Medicine Service, New Mexico VA Health Care System, Albuquerque, NM 87108, USA
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8
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Wu Z, Liu T, Chen Q, Chen T, Hu J, Sun L, Wang B, Li W, Ni J. Unveiling the unknown viral world in groundwater. Nat Commun 2024; 15:6788. [PMID: 39117653 PMCID: PMC11310336 DOI: 10.1038/s41467-024-51230-y] [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: 12/04/2023] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses as the prevailing biological entities are poorly understood in underground realms. Here, we establish the first metagenomic Groundwater Virome Catalogue (GWVC) comprising 280,420 viral species ( ≥ 5 kb) detected from 607 monitored wells in seven geo-environmental zones throughout China. In expanding ~10-fold the global portfolio of known groundwater viruses, we uncover over 99% novel viruses and about 95% novel viral clusters. By linking viruses to hosts from 119 prokaryotic phyla, we double the number of microbial phyla known to be virus-infected in groundwater. As keystone ultrasmall symbionts in aquifers, CPR bacteria and DPANN archaea are susceptible to virulent viruses. Certain complete CPR viruses even likely infect non-CPR bacteria, while partial CPR/DPANN viruses harbor cell-surface modification genes that assist symbiont cell adhesion to free-living microbes. This study reveals the unknown viral world and auxiliary metabolism associated with methane, nitrogen, sulfur, and phosphorus cycling in groundwater, and highlights the importance of subsurface virosphere in viral ecology.
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Affiliation(s)
- Zongzhi Wu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
- Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Tang Liu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518060, PR China
| | - Qian Chen
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
- Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Tianyi Chen
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
| | - Jinyun Hu
- Environmental Microbiome and Innovative Genomics Laboratory, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, PR China
| | - Liyu Sun
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
| | - Bingxue Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
| | - Wenpeng Li
- Center for Groundwater Monitoring, China Institute of Geo-environmental Monitoring, Beijing, 100081, PR China
| | - Jinren Ni
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China.
- College of Environmental Sciences and Engineering, Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, PR China.
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9
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Huang L, Guo R, Li S, Wu X, Zhang Y, Guo S, Lv Y, Xiao Z, Kang J, Meng J, Zhou P, Ma J, You W, Zhang Y, Yu H, Zhao J, Huang G, Duan Z, Yan Q, Sun W. A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome. Nat Microbiol 2024; 9:2185-2200. [PMID: 38907008 PMCID: PMC11306104 DOI: 10.1038/s41564-024-01751-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 05/01/2024] [Indexed: 06/23/2024]
Abstract
The human vagina harbours diverse microorganisms-bacteria, viruses and fungi-with profound implications for women's health. Genome-level analysis of the vaginal microbiome across multiple kingdoms remains limited. Here we utilize metagenomic sequencing data and fungal cultivation to establish the Vaginal Microbial Genome Collection (VMGC), comprising 33,804 microbial genomes spanning 786 prokaryotic species, 11 fungal species and 4,263 viral operational taxonomic units. Notably, over 25% of prokaryotic species and 85% of viral operational taxonomic units remain uncultured. This collection significantly enriches genomic diversity, especially for prevalent vaginal pathogens such as BVAB1 (an uncultured bacterial vaginosis-associated bacterium) and Amygdalobacter spp. (BVAB2 and related species). Leveraging VMGC, we characterize functional traits of prokaryotes, notably Saccharofermentanales (an underexplored yet prevalent order), along with prokaryotic and eukaryotic viruses, offering insights into their niche adaptation and potential roles in the vagina. VMGC serves as a valuable resource for studying vaginal microbiota and its impact on vaginal health.
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Affiliation(s)
- Liansha Huang
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | | | - Shenghui Li
- Puensum Genetech Institute, Wuhan, China.
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.
| | - Xiaoling Wu
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | - Shumin Guo
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Ying Lv
- Department of Reproductive Health, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zhen Xiao
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jian Kang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Peng Zhou
- Department of Acupuncture, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jie Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei You
- Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yan Zhang
- Department of Traditional Chinese Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hailong Yu
- Puensum Genetech Institute, Wuhan, China
| | - Jixin Zhao
- Puensum Genetech Institute, Wuhan, China
| | - Guangrong Huang
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Zuzhen Duan
- Department of Gynecology, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China.
| | - Wen Sun
- Centre for Translational Medicine, Shenzhen Bao'an Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China.
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China.
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10
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Cui S, Guo R, Chen C, Zhang Y, Meng J, Liu L, Li Y, Kang Z, Li S, Yan Q, Ma Y. Next-Generation Sequencing for Characterizing Respiratory Tract Virome and Improving Detection of Viral Pathogens in Children With Pneumonia. Influenza Other Respir Viruses 2024; 18:e13362. [PMID: 39118486 PMCID: PMC11310556 DOI: 10.1111/irv.13362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/05/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Pneumonia is typically caused by a variety of pathogenic microorganisms. Traditional research often focuses on the infection of a few microorganisms, whereas metagenomic studies focus on the impact of the bacteriome and mycobiome on respiratory diseases. Reports on the virome characteristics of pediatric pneumonia remain relatively scarce. METHODS We employed de novo assembly and combined homology- and feature-based methods to characterize the respiratory virome in whole-genome DNA sequencing samples from oropharynx (OP) swabs, nasopharynx (NP) swabs, and bronchoalveolar lavage fluids (BALF) of children with pneumonia. RESULTS Significant differences were observed in the alpha and beta diversity indexes, as well as in the composition of the oropharyngeal virome, between pneumonia cases and controls. We identified 1137 viral operational taxonomic units (vOTUs) with significant differences, indicating a preference of pneumonia-reduced vOTUs for infecting Prevotella, Neisseria, and Veillonella, whereas pneumonia-enriched vOTUs included polyomavirus, human adenovirus, and phages targeting Staphylococcus, Streptococcus, Granulicatella, and Actinomyces. Comparative analysis revealed higher relative abundances and prevalence rates of pneumonia-enriched OP vOTUs in NP and BALF samples compared to pneumonia-reduced vOTUs. Additionally, virome analysis identified six pediatric patients with severe human adenovirus or polyomavirus infections, five of whom might have been undetected by targeted polymerase chain reaction (PCR)-based testing. CONCLUSIONS This study offers insights into pediatric pneumonia respiratory viromes, highlighting frequent transmission of potentially pathogenic viruses and demonstrating virome analysis as a valuable adjunct for pathogen detection.
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Affiliation(s)
- Song Cui
- Department of Biochemistry and Molecular Biology, College of Basic SciencesDalian Medical UniversityDalianChina
- Department of Critical Care MedicineDalian Municipal Central HospitalDalianChina
| | | | - Changming Chen
- Department of Rheumatology and ImmunologyThe Second Affiliated Hospital of Guizhou University of Traditional Chinese MedicineGuiyangChina
| | - Yue Zhang
- Puensum Genetech InstituteWuhanChina
| | | | - Lanxin Liu
- Department of Critical Care MedicineDalian Municipal Central HospitalDalianChina
| | - Yanxia Li
- Department of Critical Care MedicineDalian Municipal Central HospitalDalianChina
| | - Zhijie Kang
- Department of HematologyThe Second Hospital of Dalian Medical UniversityDalianChina
| | | | - Qiulong Yan
- Department of Microbiology, College of Basic SciencesDalian Medical UniversityDalianChina
| | - Yufang Ma
- Department of Biochemistry and Molecular Biology, College of Basic SciencesDalian Medical UniversityDalianChina
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11
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Martin C, Gitter A, Anantharaman K. Protein Set Transformer: A protein-based genome language model to power high diversity viromics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605391. [PMID: 39131363 PMCID: PMC11312453 DOI: 10.1101/2024.07.26.605391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.
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Affiliation(s)
- Cody Martin
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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12
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de Jonge PA, van den Born BJH, Zwinderman AH, Nieuwdorp M, Dutilh BE, Herrema H. Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage. Nat Commun 2024; 15:6346. [PMID: 39068184 PMCID: PMC11283538 DOI: 10.1038/s41467-024-50777-0] [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: 12/12/2023] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Viruses are core components of the human microbiome, impacting health through interactions with gut bacteria and the immune system. Most human microbiome viruses are bacteriophages, which exclusively infect bacteria. Until recently, most gut virome studies focused on low taxonomic resolution (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified an expansive and widespread bacteriophage lineage in inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in various human populations. Based on a phylogeny using sequences from six viral genome databases, we propose the Candidatus order Heliusvirales. We identify heliusviruses in 82% of 5441 individuals across 39 studies, and in nine metagenomes from humans that lived in Europe and North America between 1000 and 5000 years ago. We show that a large lineage started to diversify when Homo sapiens first appeared some 300,000 years ago. Ancient peoples and modern hunter-gatherers have distinct Ca. Heliusvirales populations with lower richness than modern urbanized people. Urbanized people suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles.
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Affiliation(s)
- Patrick A de Jonge
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Bert-Jan H van den Born
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology; Biostatistics and Bioinformatics; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics; Science for Life, Utrecht University, Utrecht, the Netherlands
- Institute of Biodiversity; Faculty of Biological Sciences; Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
| | - Hilde Herrema
- Department of Internal and Experimental Vascular Medicine; Amsterdam UMC; Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Gastroenterology, Endocrinology & Metabolism; Endocrinology, Metabolism & Nutrition, Amsterdam UMC, Amsterdam, the Netherlands.
- Amsterdam Cardiovascular Sciences; Diabetes & Metabolism, Amsterdam UMC, Amsterdam, the Netherlands.
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13
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Vakirlis N, Kupczok A. Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins. Genome Res 2024; 34:888-903. [PMID: 38977308 PMCID: PMC11293555 DOI: 10.1101/gr.278977.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024]
Abstract
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.
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Affiliation(s)
- Nikolaos Vakirlis
- Institute For Fundamental Biomedical Research, B.S.R.C. "Alexander Fleming," Vari 166 72, Greece;
- Institute for General Microbiology, Kiel University, 24118 Kiel, Germany
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, 6700 PB Wageningen, The Netherlands
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14
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Tian X, Li S, Wang C, Zhang Y, Feng X, Yan Q, Guo R, Wu F, Wu C, Wang Y, Huo X, Ma X. Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. MICROBIOME 2024; 12:130. [PMID: 39026313 PMCID: PMC11256409 DOI: 10.1186/s40168-024-01832-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: 10/31/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.
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Affiliation(s)
- Xiangge Tian
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Chao Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yanyan Zhang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Chunxue Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Yan Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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15
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Chibani CM, Shah SA, Schmitz RA, Nayfach S. Inaccurate viral prediction leads to overestimated diversity of the archaeal virome in the human gut. Nat Commun 2024; 15:5976. [PMID: 39019907 PMCID: PMC11255274 DOI: 10.1038/s41467-024-49902-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 06/24/2024] [Indexed: 07/19/2024] Open
Affiliation(s)
- Cynthia M Chibani
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, D-24118, Kiel, Germany
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Ruth A Schmitz
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, D-24118, Kiel, Germany
| | - Stephen Nayfach
- Profluent Bio, Berkeley, CA, USA.
- Joint Genome Institute, Berkeley, CA, USA.
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16
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Dong Y, Chen WH, Zhao XM. VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes. Genome Biol 2024; 25:177. [PMID: 38965579 PMCID: PMC11229495 DOI: 10.1186/s13059-024-03320-9] [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: 12/18/2023] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Identifying viruses from metagenomes is a common step to explore the virus composition in the human gut. Here, we introduce VirRep, a hybrid language representation learning framework, for identifying viruses from human gut metagenomes. VirRep combines a context-aware encoder and an evolution-aware encoder to improve sequence representation by incorporating k-mer patterns and sequence homologies. Benchmarking on both simulated and real datasets with varying viral proportions demonstrates that VirRep outperforms state-of-the-art methods. When applied to fecal metagenomes from a colorectal cancer cohort, VirRep identifies 39 high-quality viral species associated with the disease, many of which cannot be detected by existing methods.
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Affiliation(s)
- Yanqi Dong
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
| | - Xing-Ming Zhao
- Department of Neurology, Zhongshan Hospital and Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
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17
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Sardar P, Almeida A, Pedicord VA. Integrating functional metagenomics to decipher microbiome-immune interactions. Immunol Cell Biol 2024. [PMID: 38952337 DOI: 10.1111/imcb.12798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.
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Affiliation(s)
- Puspendu Sardar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge School of Biological Sciences, Cambridge, UK
| | - Virginia A Pedicord
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
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18
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Sun CL, Pratama AA, Gazitúa MC, Cronin D, McGivern BB, Wainaina JM, Vik DR, Zayed AA, Bolduc B, Wrighton KC, Rich VI, Sullivan MB. Virus ecology and 7-year temporal dynamics across a permafrost thaw gradient. Environ Microbiol 2024; 26:e16665. [PMID: 39101434 DOI: 10.1111/1462-2920.16665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 05/16/2024] [Indexed: 08/06/2024]
Abstract
Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth-related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon-degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long-term observations enhance our understanding of soil viruses in the context of climate-relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.
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Affiliation(s)
- Christine L Sun
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | | | - Dylan Cronin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Bridget B McGivern
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - James M Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
| | - Dean R Vik
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Benjamin Bolduc
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
| | - Kelly C Wrighton
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, USA
- National Science Foundation EMERGE Biology Integration Institute, The Ohio State University, Columbus, USA
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, Ohio, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio, USA
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19
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Graham EB, Camargo AP, Wu R, Neches RY, Nolan M, Paez-Espino D, Kyrpides NC, Jansson JK, McDermott JE, Hofmockel KS. A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nat Microbiol 2024; 9:1873-1883. [PMID: 38902374 PMCID: PMC11222151 DOI: 10.1038/s41564-024-01686-x] [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: 09/17/2023] [Accepted: 03/25/2024] [Indexed: 06/22/2024]
Abstract
Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
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Affiliation(s)
- Emily B Graham
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
| | - Antonio Pedro Camargo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Russell Y Neches
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Matt Nolan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikos C Kyrpides
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Agronomy, Iowa State University, Ames, IA, USA
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20
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Tierney BT, Kim J, Overbey EG, Ryon KA, Foox J, Sierra MA, Bhattacharya C, Damle N, Najjar D, Park J, Garcia Medina JS, Houerbi N, Meydan C, Wain Hirschberg J, Qiu J, Kleinman AS, Al-Ghalith GA, MacKay M, Afshin EE, Dhir R, Borg J, Gatt C, Brereton N, Readhead BP, Beyaz S, Venkateswaran KJ, Wiseman K, Moreno J, Boddicker AM, Zhao J, Lajoie BR, Scott RT, Altomare A, Kruglyak S, Levy S, Church GM, Mason CE. Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight. Nat Microbiol 2024; 9:1661-1675. [PMID: 38862604 PMCID: PMC11222149 DOI: 10.1038/s41564-024-01635-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/09/2024] [Indexed: 06/13/2024]
Abstract
Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes. However, documenting microbial shifts during spaceflight has been difficult due to mission constraints that lead to limited sampling and profiling. Here we executed a six-month longitudinal study to quantify the high-resolution human microbiome response to three days in orbit for four individuals. Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, we characterized time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. We found that most alterations were transient across body sites; for example, viruses increased in skin sites mostly during flight. However, longer-term shifts were observed in the oral microbiome, including increased plaque-associated bacteria (for example, Fusobacteriota), which correlated with immune cell gene expression. Further, microbial genes associated with phage activity, toxin-antitoxin systems and stress response were enriched across multiple body sites. In total, this study reveals in-depth characterization of microbiome and immune response shifts experienced by astronauts during short-term spaceflight and the associated changes to the living environment, which can help guide future missions, spacecraft design and space habitat planning.
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Affiliation(s)
- Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Eliah G Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- BioAstra, Inc., New York, NY, USA
- Center for STEM, University of Austin, Austin, TX, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Chandrima Bhattacharya
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Deena Najjar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jiwoon Park
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - J Sebastian Garcia Medina
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Nadia Houerbi
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Jake Qiu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S Kleinman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Matthew MacKay
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Raja Dhir
- Seed Health, Inc., Venice, CA, USA
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Christine Gatt
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Nicholas Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Benjamin P Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | | | | | | | - Ryan T Scott
- KBR; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | | | | | | | - George M Church
- Harvard Medical School and the Wyss Institute, Boston, MA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- BioAstra, Inc., New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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Chen CM, Yan QL, Guo RC, Tang F, Wang MH, Yi HZ, Huang CX, Liu C, Wang QY, Lan WY, Jiang Z, Yang YZ, Wang GY, Zhang AQ, Ma J, Zhang Y, You W, Ullah H, Zhang Y, Li SH, Yao XM, Sun W, Ma WK. Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis. J Transl Med 2024; 22:564. [PMID: 38872164 PMCID: PMC11170907 DOI: 10.1186/s12967-024-05374-6] [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: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND/PURPOSE(S) The gut microbiota and its metabolites play crucial roles in pathogenesis of arthritis, highlighting gut microbiota as a promising avenue for modulating autoimmunity. However, the characterization of the gut virome in arthritis patients, including osteoarthritis (OA) and gouty arthritis (GA), requires further investigation. METHODS We employed virus-like particle (VLP)-based metagenomic sequencing to analyze gut viral community in 20 OA patients, 26 GA patients, and 31 healthy controls, encompassing a total of 77 fecal samples. RESULTS Our analysis generated 6819 vOTUs, with a considerable proportion of viral genomes differing from existing catalogs. The gut virome in OA and GA patients differed significantly from healthy controls, showing variations in diversity and viral family abundances. We identified 157 OA-associated and 94 GA-associated vOTUs, achieving high accuracy in patient-control discrimination with random forest models. OA-associated viruses were predicted to infect pro-inflammatory bacteria or bacteria associated with immunoglobulin A production, while GA-associated viruses were linked to Bacteroidaceae or Lachnospiraceae phages. Furthermore, several viral functional orthologs displayed significant differences in frequency between OA-enriched and GA-enriched vOTUs, suggesting potential functional roles of these viruses. Additionally, we trained classification models based on gut viral signatures to effectively discriminate OA or GA patients from healthy controls, yielding AUC values up to 0.97, indicating the clinical utility of the gut virome in diagnosing OA or GA. CONCLUSION Our study highlights distinctive alterations in viral diversity and taxonomy within gut virome of OA and GA patients, offering insights into arthritis etiology and potential treatment and prevention strategies.
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Affiliation(s)
- Chang-Ming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiu-Long Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Fang Tang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Min-Hui Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Han-Zhi Yi
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chun-Xia Huang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Can Liu
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiu-Yi Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wei-Ya Lan
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Zong Jiang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yu-Zheng Yang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Guang-Yang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Jie Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yan Zhang
- Department of Traditional Chinese Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wei You
- Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | | | - Xue-Ming Yao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Wen Sun
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China.
| | - Wu-Kai Ma
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China.
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Handa S, Biswas T, Chakraborty J, Ghosh G, Paul BG, Ghosh P. Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.23.563531. [PMID: 37961358 PMCID: PMC10634737 DOI: 10.1101/2023.10.23.563531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Diversity-generating retroelements (DGRs) create massive protein sequence variation in ecologically diverse microbes. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypical Bordetella bacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for cDNA synthesis by the reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Cryo-EM revealed that this RNA enveloped bRT and lay over barrel-shaped Avd, forming an intimate ribonucleoprotein (RNP). An abundance of essential interactions between RNA structural elements and bRT-Avd precisely positioned an RNA homoduplex for initiation of cDNA synthesis by cis -priming. Our results explain how the surrounding RNA primes cDNA synthesis, promotes processivity, terminates polymerization, and strictly limits mutagenesis to select proteins through mechanisms that are likely conserved in DGRs from distant taxa.
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23
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Hu J, Chen J, Nie Y, Zhou C, Hou Q, Yan X. Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs. MICROBIOME 2024; 12:102. [PMID: 38840247 DOI: 10.1186/s40168-024-01818-9] [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: 12/30/2023] [Accepted: 04/18/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Mammalian intestine harbors a mass of phages that play important roles in maintaining gut microbial ecosystem and host health. Pig has become a common model for biomedical research and provides a large amount of meat for human consumption. However, the knowledge of gut phages in pigs is still limited. RESULTS Here, we investigated the gut phageome in 112 pigs from seven pig breeds using PhaBOX strategy based on the metagenomic data. A total of 174,897 non-redundant gut phage genomes were assembled from 112 metagenomes. A total of 33,487 gut phage genomes were classified and these phages mainly belonged to phage families such as Ackermannviridae, Straboviridae, Peduoviridae, Zierdtviridae, Drexlerviridae, and Herelleviridae. The gut phages in seven pig breeds exhibited distinct communities and the gut phage communities changed with the age of pig. These gut phages were predicted to infect a broad range of 212 genera of prokaryotes, such as Candidatus Hamiltonella, Mycoplasma, Colwellia, and Lactobacillus. The data indicated that broad KEGG and CAZy functions were also enriched in gut phages of pigs. The gut phages also carried the antimicrobial resistance genes (ARGs) and the most abundant antimicrobial resistance genotype was diaminopyrimidine resistance. CONCLUSIONS Our research delineates a landscape for gut phages in seven pig breeds and reveals that gut phages serve as a key reservoir of ARGs in pigs. Video Abstract.
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Affiliation(s)
- Jun Hu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei, 430070, China
| | - Jianwei Chen
- BGI Research, Qingdao, Shandong, 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Yangfan Nie
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | | | - Qiliang Hou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei, 430070, China
| | - Xianghua Yan
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Frontiers Science Center for Animal Breeding and Sustainable Production, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei, 430070, China.
- Hubei Provincial Engineering Laboratory for Pig Precision Feeding and Feed Safety Technology, Wuhan, Hubei, 430070, China.
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24
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Zhang J, Tang A, Jin T, Sun D, Guo F, Lei H, Lin L, Shu W, Yu P, Li X, Li B. A panoramic view of the virosphere in three wastewater treatment plants by integrating viral-like particle-concentrated and traditional non-concentrated metagenomic approaches. IMETA 2024; 3:e188. [PMID: 38898980 PMCID: PMC11183165 DOI: 10.1002/imt2.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 06/21/2024]
Abstract
Wastewater biotreatment systems harbor a rich diversity of microorganisms, and the effectiveness of biotreatment systems largely depends on the activity of these microorganisms. Specifically, viruses play a crucial role in altering microbial behavior and metabolic processes throughout their infection phases, an aspect that has recently attracted considerable interest. Two metagenomic approaches, viral-like particle-concentrated (VPC, representing free viral-like particles) and non-concentrated (NC, representing the cellular fraction), were employed to assess their efficacy in revealing virome characteristics, including taxonomy, diversity, host interactions, lifestyle, dynamics, and functional genes across processing units of three wastewater treatment plants (WWTPs). Our findings indicate that each approach offers unique insights into the viral community and functional composition. Their combined use proved effective in elucidating WWTP viromes. We identified nearly 50,000 viral contigs, with Cressdnaviricota and Uroviricota being the predominant phyla in the VPC and NC fractions, respectively. Notably, two pathogenic viral families, Asfarviridae and Adenoviridae, were commonly found in these WWTPs. We also observed significant differences in the viromes of WWTPs processing different types of wastewater. Additionally, various phage-derived auxiliary metabolic genes (AMGs) were active at the RNA level, contributing to the metabolism of the microbial community, particularly in carbon, sulfur, and phosphorus cycling. Moreover, we identified 29 virus-carried antibiotic resistance genes (ARGs) with potential for host transfer, highlighting the role of viruses in spreading ARGs in the environment. Overall, this study provides a detailed and integrated view of the virosphere in three WWTPs through the application of VPC and NC metagenomic approaches. Our findings enhance the understanding of viral communities, offering valuable insights for optimizing the operation and regulation of wastewater treatment systems.
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Affiliation(s)
- Jiayu Zhang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
- Research Center for Eco‐Environmental EngineeringDongguan University of TechnologyDongguanChina
| | - Aixi Tang
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Tao Jin
- Guangdong Magigene Biotechnology Co., Ltd.ShenzhenChina
| | - Deshou Sun
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
- Shenzhen Tongchen Biotechnology Co., LimitedShenzhenChina
| | - Fangliang Guo
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Huaxin Lei
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Lin Lin
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Wensheng Shu
- Guangdong Magigene Biotechnology Co., Ltd.ShenzhenChina
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life SciencesSouth China Normal UniversityGuangzhouChina
| | - Pingfeng Yu
- College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
| | - Xiaoyan Li
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Bing Li
- Institute of Environment and Ecology, Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
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25
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Gao Y, Zhong Z, Zhang D, Zhang J, Li YX. Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining. MICROBIOME 2024; 12:94. [PMID: 38790030 PMCID: PMC11118758 DOI: 10.1186/s40168-024-01807-y] [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: 11/11/2023] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising source of therapeutic agents due to their structural diversity and functional versatility. However, their biosynthetic capacity and ecological functions remain largely underexplored. RESULTS Here, we aim to explore the biosynthetic profile of RiPPs and their potential roles in the interactions between microbes and viruses in the ocean, which encompasses a vast diversity of unique biomes that are rich in interactions and remains chemically underexplored. We first developed TrRiPP to identify RiPPs from ocean metagenomes, a deep learning method that detects RiPP precursors in a hallmark gene-independent manner to overcome the limitations of classic methods in processing highly fragmented metagenomic data. Applying this method to metagenomes from the global ocean microbiome, we uncover a diverse array of previously uncharacterized putative RiPP families with great novelty and diversity. Through correlation analysis based on metatranscriptomic data, we observed a high prevalence of antiphage defense-related and phage-related protein families that were co-expressed with RiPP families. Based on this putative association between RiPPs and phage infection, we constructed an Ocean Virus Database (OVD) and established a RiPP-involving host-phage interaction network through host prediction and co-expression analysis, revealing complex connectivities linking RiPP-encoding prokaryotes, RiPP families, viral protein families, and phages. These findings highlight the potential of RiPP families involved in prokaryote-phage interactions and coevolution, providing insights into their ecological functions in the ocean microbiome. CONCLUSIONS This study provides a systematic investigation of the biosynthetic potential of RiPPs from the ocean microbiome at a global scale, shedding light on the essential insights into the ecological functions of RiPPs in prokaryote-phage interactions through the integration of deep learning approaches, metatranscriptomic data, and host-phage connectivity. This study serves as a valuable example of exploring the ecological functions of bacterial secondary metabolites, particularly their associations with unexplored microbial interactions. Video Abstract.
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Affiliation(s)
- Ying Gao
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Zheng Zhong
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Dengwei Zhang
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Jian Zhang
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China
| | - Yong-Xin Li
- CYM305, Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, 999077, China.
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Xiao Z, Zhang Y, Zhang W, Zhang A, Wang G, Chen C, Ullah H, Ayaz T, Li S, Zhaxi D, Yan Q, Kang J, Xu X. Characterizations of gut bacteriome, mycobiome, and virome of healthy individuals living in sea-level and high-altitude areas. Int Microbiol 2024:10.1007/s10123-024-00531-9. [PMID: 38758414 DOI: 10.1007/s10123-024-00531-9] [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: 12/27/2023] [Revised: 04/05/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood. METHODS Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants. RESULTS The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses. CONCLUSION The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.
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Affiliation(s)
- Zhen Xiao
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Wei Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Aiqin Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, 550003, China
| | - Hayan Ullah
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Taj Ayaz
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430010, China
| | - Duoji Zhaxi
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Jian Kang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaoguang Xu
- Institute of High-Altitude Medicine, People's Hospital of Nagqu Affiliated to Dalian Medical University, Nagqu, 852099, China.
- Department of Neurosurgery, Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China.
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27
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Wilde J, Boyes R, Robinson AV, Daisley BA, Botschner AJ, Brettingham DJL, Macpherson CV, Mallory E, Allen-Vercoe E. Assessing phage-host population dynamics by reintroducing virulent viruses to synthetic microbiomes. Cell Host Microbe 2024; 32:768-778.e9. [PMID: 38653241 DOI: 10.1016/j.chom.2024.04.001] [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: 09/29/2023] [Revised: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
Microbiomes feature complex interactions between diverse bacteria and bacteriophages. Synthetic microbiomes offer a powerful way to study these interactions; however, a major challenge is obtaining a representative bacteriophage population during the bacterial isolation process. We demonstrate that colony isolation reliably excludes virulent viruses from sample sources with low virion-to-bacteria ratios such as feces, creating "virulent virus-free" controls. When the virulent dsDNA virome is reintroduced to a 73-strain synthetic gut microbiome in a bioreactor model of the human colon, virulent viruses target susceptible strains without significantly altering community structure or metabolism. In addition, we detected signals of prophage induction that associate with virulent predation. Overall, our findings indicate that dilution-based isolation methods generate synthetic gut microbiomes that are heavily depleted, if not devoid, of virulent viruses and that such viruses, if reintroduced, have a targeted effect on community assembly, metabolism, and prophage replication.
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Affiliation(s)
- Jacob Wilde
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Randy Boyes
- Queen's University, Department of Community Health and Epidemiology, Kingston, ON K7L 3N6, Canada
| | - Avery V Robinson
- University of Oxford, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford OX3 7FY, UK
| | - Brendan A Daisley
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Alexander J Botschner
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Dylan J L Brettingham
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Christine V Macpherson
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Elizabeth Mallory
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Emma Allen-Vercoe
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada.
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28
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Zhao F, Wang J. Another piece of puzzle for the human microbiome: the gut virome under dietary modulation. J Genet Genomics 2024:S1673-8527(24)00098-5. [PMID: 38710286 DOI: 10.1016/j.jgg.2024.04.013] [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: 03/02/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024]
Abstract
The virome is the most abundant and highly variable microbial consortium in the gut. Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes, the virome has remained a relatively elusive aspect of the human microbiome. In recent years, studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health. Here, we review the responses of the gut virome to dietary intake and the potential health implications, presenting changes in the gut viral community and preferences of viral members to particular diets. We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota. We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer, as well as the import of new viral members along with the diet. Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary interventions and health maintenance strategies targeting the gut microbiota.
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Affiliation(s)
- Fengxiang Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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29
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Lee S, Kim G, Karin EL, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, Steinegger M. Petabase-Scale Homology Search for Structure Prediction. Cold Spring Harb Perspect Biol 2024; 16:a041465. [PMID: 38316555 PMCID: PMC11065157 DOI: 10.1101/cshperspect.a041465] [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] [Indexed: 02/07/2024]
Abstract
The recent CASP15 competition highlighted the critical role of multiple sequence alignments (MSAs) in protein structure prediction, as demonstrated by the success of the top AlphaFold2-based prediction methods. To push the boundaries of MSA utilization, we conducted a petabase-scale search of the Sequence Read Archive (SRA), resulting in gigabytes of aligned homologs for CASP15 targets. These were merged with default MSAs produced by ColabFold-search and provided to ColabFold-predict. By using SRA data, we achieved highly accurate predictions (GDT_TS > 70) for 66% of the non-easy targets, whereas using ColabFold-search default MSAs scored highly in only 52%. Next, we tested the effect of deep homology search and ColabFold's advanced features, such as more recycles, on prediction accuracy. While SRA homologs were most significant for improving ColabFold's CASP15 ranking from 11th to 3rd place, other strategies contributed too. We analyze these in the context of existing strategies to improve prediction.
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Affiliation(s)
- Sewon Lee
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Gyuri Kim
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | | | - Milot Mirdita
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
| | - Sukhwan Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, South Korea
| | - Rayan Chikhi
- Institut Pasteur, Université Paris Cité, G5 Sequence Bioinformatics, 75015 Paris, France
| | - Artem Babaian
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Gwanak-gu, Seoul 08826, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul 08826, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
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30
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Zheng L, Shen J, Chen R, Hu Y, Zhao W, Leung ELH, Dai L. Genome engineering of the human gut microbiome. J Genet Genomics 2024; 51:479-491. [PMID: 38218395 DOI: 10.1016/j.jgg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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Affiliation(s)
- Linggang Zheng
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruiyue Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucan Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Science, University of Macau, Macau 999078, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Barcenilla C, Cobo-Díaz JF, De Filippis F, Valentino V, Cabrera Rubio R, O'Neil D, Mahler de Sanchez L, Armanini F, Carlino N, Blanco-Míguez A, Pinto F, Calvete-Torre I, Sabater C, Delgado S, Ruas-Madiedo P, Quijada NM, Dzieciol M, Skírnisdóttir S, Knobloch S, Puente A, López M, Prieto M, Marteinsson VT, Wagner M, Margolles A, Segata N, Cotter PD, Ercolini D, Alvarez-Ordóñez A. Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments. Nat Protoc 2024; 19:1291-1310. [PMID: 38267717 DOI: 10.1038/s41596-023-00949-x] [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: 03/23/2023] [Accepted: 11/09/2023] [Indexed: 01/26/2024]
Abstract
Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.
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Affiliation(s)
- Coral Barcenilla
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | | | | | | | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Niccolò Carlino
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Aitor Blanco-Míguez
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Inés Calvete-Torre
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Carlos Sabater
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Susana Delgado
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Narciso M Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Monika Dzieciol
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Stephen Knobloch
- Microbiology Research Group, Matís ohf., Reykjavík, Iceland
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Alba Puente
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Viggó Thór Marteinsson
- Microbiology Research Group, Matís ohf., Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Abelardo Margolles
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario, Oviedo, Asturias, Spain
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland and VistaMilk Research Centres, Cork, Ireland
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain.
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32
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Wu Y, Peng Y. Ten computational challenges in human virome studies. Virol Sin 2024:S1995-820X(24)00068-3. [PMID: 38697263 DOI: 10.1016/j.virs.2024.04.008] [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: 01/10/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024] Open
Abstract
In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent, primarily hindered by the absence of effective methods, particularly in the domain of computational tools. This perspective systematically outlines ten computational challenges spanning various types of virome studies. These challenges arise due to the vast diversity of viromes, the absence of a universal marker gene in viral genomes, the low abundance of virus populations, the remote or minimal homology of viral proteins to known proteins, and the highly dynamic and heterogeneous nature of viromes. For each computational challenge, we discuss the underlying reasons, current research progress, and potential solutions. The resolution of these challenges necessitates ongoing collaboration among computational scientists, virologists, and multidisciplinary experts. In essence, this perspective serves as a comprehensive guide for directing computational efforts in human virome studies.
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Affiliation(s)
- Yifan Wu
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China
| | - Yousong Peng
- Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China.
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33
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Ullah Khan N, Sadiq A, Khan J, Basharat N, Hassan ZU, Ali I, Shah TA, Bourhia M, Bin Jardan YA, Wondmie GF. Molecular characterization of plasma virome of hepatocellular carcinoma (HCC) patients. AMB Express 2024; 14:46. [PMID: 38664337 PMCID: PMC11045709 DOI: 10.1186/s13568-024-01696-2] [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: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the most common cancer type, arising from various causes, and responsible for a substantial number of cancer-related fatalities. Recent advancements in viral metagenomics have empowered scientists to delve into the intricate diversity of the virosphere, viral evolution, interactions between viruses and their hosts, and the identification of viral causes behind disease outbreaks, the development of specific symptoms, and their potential role in altering the host's physiology. The present study had the objective of "Molecular Characterization of HBV, HCV, anelloviruses, CMV, SENV-D, SENV-H, HEV, and HPV viruses among individuals suffering from HCC." A total of 381 HCC patients contributed 10 cc of blood each for this study. The research encompassed the assessment of tumor markers, followed by molecular characterization of HBV, HCV, Anelloviruses (TTV, TTMV, and TTMDV), SENV-H and SENV-D viruses, HEV, CMV, and HPV, as well as histopathological examinations. The outcomes of this study revealed that majority of the HCC patients 72.4% (276/381) were male as compared to females. HCV infection, at 76.4% (291 out of 381), exhibited a significant association (p < 0.05) with HCC. Most patients displayed singular lesions in the liver, with Child Pugh Score Type B being the predominant finding in 45.2% of cases. Plasma virome analysis indicated the prevalence of TTMDV (75%), followed by TTMV (70%) and TTV (42.1%) among anelloviruses in HCC patients. Similarly, SENV-H (52%) was followed by SENV-D (20%), with co-infections at 15%. The presence of CMV and HEV among the HCC patients was recorded 5% each however 3.5% of the patients showed the presence of HPV. In conclusion, this study underscores that HCC patients serve as reservoirs for various pathogenic and non-pathogenic viruses, potentially contributing to the development, progression, and severity of the disease.
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Affiliation(s)
- Niamat Ullah Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Asma Sadiq
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Jadoon Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan.
| | - Nosheen Basharat
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Zulfiqar Ul Hassan
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan
| | - Ijaz Ali
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
- Center for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, West Mishref, Kuwait
| | - Tawaf Ali Shah
- College of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, 80060, Morocco.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
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Lv LJ, Wen JY, Zhang Y, Guo RC, Li H, Yi ZT, He TW, Chen MC, Chen Y, Wu XY, Li SH, Kang J, Hou YP, Yan QL, Yin AH. Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia. mSphere 2024; 9:e0067623. [PMID: 38506520 PMCID: PMC11036803 DOI: 10.1128/msphere.00676-23] [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: 11/05/2023] [Accepted: 12/21/2023] [Indexed: 03/21/2024] Open
Abstract
Preeclampsia (PE), a pregnancy-specific syndrome, has been associated with the gut bacteriome. Here, to investigate the impact of the gut virome on the development of PE, we identified over 8,000 nonredundant viruses from the fecal metagenomes of 40 early-onset PE and 37 healthy pregnant women and profiled their abundances. Comparison and correlation analysis showed that PE-enriched viruses frequently connected to Blautia species enriched in PE. By contrast, bacteria linked to PE-depleted viruses were often the Bacteroidaceae members such as Bacteroides spp., Phocaeicola spp., Parabacteroides spp., and Alistipes shahii. In terms of viral function, PE-depleted viruses had auxiliary metabolic genes that participated in the metabolism of simple and complex polysaccharides, sulfur metabolism, lipopolysaccharide biosynthesis, and peptidoglycan biosynthesis, while PE-enriched viruses had a gene encoding cyclic pyranopterin monophosphate synthase, which seemed to be special, that participates in the biosynthesis of the molybdenum cofactor. Furthermore, the classification model based on gut viral signatures was developed to discriminate PE patients from healthy controls and showed an area under the receiver operating characteristic curve of 0.922 that was better than that of the bacterium-based model. This study opens up new avenues for further research, providing valuable insights into the PE gut virome and offering potential directions for future mechanistic and therapeutic investigations, with the ultimate goal of improving the diagnosis and management of PE.IMPORTANCEThe importance of this study lies in its exploration of the previously overlooked but potentially critical role of the gut virome in preeclampsia (PE). While the association between PE and the gut bacteriome has been recognized, this research takes a pioneering step into understanding how the gut virome, represented by over 8,000 nonredundant viruses, contributes to this condition. The findings reveal intriguing connections between PE-enriched viruses and specific gut bacteria, such as the prevalence of Blautia species in individuals with PE, contrasting with bacteria linked to PE-depleted viruses, including members of the Bacteroidaceae family. These viral interactions and associations provide a deeper understanding of the complex dynamics at play in PE.
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Affiliation(s)
- Li-Juan Lv
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Ji-Ying Wen
- Department of Obstetrics, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, China
| | | | - Hui Li
- Department of Obstetrics, Guangdong Women and Children Hospital, Guangzhou, China
| | - Zhou-Ting Yi
- Department of Obstetrics, Guangdong Women and Children Hospital, Guangzhou, China
| | - Tian-Wen He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Min-Chai Chen
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yang Chen
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiao-Yan Wu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | | | - Jian Kang
- Department of Microbiology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Ya-Ping Hou
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Qiu-long Yan
- Department of Microbiology, College of Basic Medical Science, Dalian Medical University, Dalian, China
| | - Ai-Hua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
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35
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Xu Q, Zhang H, Vandenkoornhuyse P, Guo S, Kuzyakov Y, Shen Q, Ling N. Carbon starvation raises capacities in bacterial antibiotic resistance and viral auxiliary carbon metabolism in soils. Proc Natl Acad Sci U S A 2024; 121:e2318160121. [PMID: 38598339 PMCID: PMC11032446 DOI: 10.1073/pnas.2318160121] [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: 10/18/2023] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Organic carbon availability in soil is crucial for shaping microbial communities, yet, uncertainties persist concerning microbial adaptations to carbon levels and the ensuing ecological and evolutionary consequences. We investigated organic carbon metabolism, antibiotic resistance, and virus-host interactions in soils subjected to 40 y of chemical and organic fertilization that led to contrasting carbon availability: carbon-poor and carbon-rich soils, respectively. Carbon-poor soils drove the enrichment of putative genes involved in organic matter decomposition and exhibited specialization in utilizing complex organic compounds, reflecting scramble competition. This specialization confers a competitive advantage of microbial communities in carbon-poor soils but reduces their buffering capacity in terms of organic carbon metabolisms, making them more vulnerable to environmental fluctuations. Additionally, in carbon-poor soils, viral auxiliary metabolic genes linked to organic carbon metabolism increased host competitiveness and environmental adaptability through a strategy akin to "piggyback the winner." Furthermore, putative antibiotic resistance genes, particularly in low-abundance drug categories, were enriched in carbon-poor soils as an evolutionary consequence of chemical warfare (i.e., interference competition). This raises concerns about the potential dissemination of antibiotic resistance from conventional agriculture that relies on chemical-only fertilization. Consequently, carbon starvation resulting from long-term chemical-only fertilization increases microbial adaptations to competition, underscoring the importance of implementing sustainable agricultural practices to mitigate the emergence and spread of antimicrobial resistance and to increase soil carbon storage.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
- CNRS, UMR 6553 EcoBio, Université de Rennes, Rennes Cedex35042, France
| | - He Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou730020, China
| | | | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen37077, Germany
- Department of Agricultural Soil Science, University of Göttingen, Göttingen37077, Germany
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
| | - Ning Ling
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou730020, China
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Wu Y, Gao N, Sun C, Feng T, Liu Q, Chen WH. A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. MICROBIOME 2024; 12:69. [PMID: 38576042 PMCID: PMC10993611 DOI: 10.1186/s40168-024-01784-2] [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: 03/20/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.
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Affiliation(s)
- Yingjian Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Na Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, 264003, China.
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Flores VS, Amgarten DE, Iha BKV, Ryon KA, Danko D, Tierney BT, Mason C, da Silva AM, Setubal JC. Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium. Sci Rep 2024; 14:7913. [PMID: 38575625 PMCID: PMC10994904 DOI: 10.1038/s41598-024-58226-0] [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: 06/08/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.
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Affiliation(s)
- Vinicius S Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Deyvid E Amgarten
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Bruno Koshin Vázquez Iha
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | | | | | - Braden T Tierney
- Weill Cornell Medicine, New York, NY, USA
- Harvard Medical School, Cambridge, MA, USA
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil.
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Pinto Y, Chakraborty M, Jain N, Bhatt AS. Phage-inclusive profiling of human gut microbiomes with Phanta. Nat Biotechnol 2024; 42:651-662. [PMID: 37231259 DOI: 10.1038/s41587-023-01799-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.
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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
| | | | - Navami Jain
- 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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Chen J, Sun C, Dong Y, Jin M, Lai S, Jia L, Zhao X, Wang H, Gao NL, Bork P, Liu Z, Chen W, Zhao X. Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305818. [PMID: 38240578 PMCID: PMC10987132 DOI: 10.1002/advs.202305818] [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: 08/18/2023] [Revised: 12/01/2023] [Indexed: 04/04/2024]
Abstract
Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.
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Affiliation(s)
- Jingchao Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Yanqi Dong
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Menglu Jin
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Senying Lai
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Longhao Jia
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
| | - Xueyang Zhao
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
| | - Huarui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
| | - Na L. Gao
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- Department of Laboratory MedicineZhongnan Hospital of Wuhan UniversityWuhan UniversityWuhan430071China
| | - Peer Bork
- European Molecular Biology LaboratoryStructural and Computational Biology Unit69117HeidelbergGermany
- Max Delbrück Centre for Molecular Medicine13125BerlinGermany
- Yonsei Frontier Lab (YFL)Yonsei University03722SeoulSouth Korea
- Department of BioinformaticsBiocenterUniversity of Würzburg97070WürzburgGermany
| | - Zhi Liu
- Department of BiotechnologyCollege of Life Science and TechnologyHuazhong University of Science and Technology430074WuhanChina
| | - Wei‐Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of EducationHubei Key Laboratory of Bioinformatics and Molecular ImagingCenter for Artificial Intelligence BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanHubei430074China
- College of Life ScienceHenan Normal UniversityXinxiangHenan453007China
- Institution of Medical Artificial IntelligenceBinzhou Medical UniversityYantai264003China
| | - Xing‐Ming Zhao
- Department of NeurologyZhongshan Hospital and Institute of Science and Technology for Brain‐Inspired IntelligenceFudan UniversityShanghai200433China
- MOE Key Laboratory of Computational Neuroscience and Brain‐Inspired Intelligenceand MOE Frontiers Center for Brain ScienceFudan UniversityShanghai200433China
- State Key Laboratory of Medical NeurobiologyInstitute of Brain ScienceFudan UniversityShanghai200433China
- International Human Phenome Institutes (Shanghai)Shanghai200433China
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40
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Ma B, Wang Y, Zhao K, Stirling E, Lv X, Yu Y, Hu L, Tang C, Wu C, Dong B, Xue R, Dahlgren RA, Tan X, Dai H, Zhu YG, Chu H, Xu J. Biogeographic patterns and drivers of soil viromes. Nat Ecol Evol 2024; 8:717-728. [PMID: 38383853 DOI: 10.1038/s41559-024-02347-2] [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: 04/26/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Erinne Stirling
- Agriculture and Food, CSIRO, Adelaide, South Australia, Australia
- Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, China
| | - Yijun Yu
- Arable Soil Quality and Fertilizer Administration Bureau of Zhejiang Province, Hangzhou, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Chao Tang
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Chuyi Wu
- School of Earth Sciences, Zhejiang University, Hangzhou, China
| | - Baiyu Dong
- Institute of Applied Remote Sensing and Information Technology, Zhejiang University, Hangzhou, China
| | - Ran Xue
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, CA, USA
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hengyi Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Yong-Guan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China.
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41
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Liu X, Liu Y, Liu J, Zhang H, Shan C, Guo Y, Gong X, Cui M, Li X, Tang M. Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence. Neural Regen Res 2024; 19:833-845. [PMID: 37843219 PMCID: PMC10664138 DOI: 10.4103/1673-5374.382223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/19/2023] [Accepted: 06/17/2023] [Indexed: 10/17/2023] Open
Abstract
A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chaofan Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yinglu Guo
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xun Gong
- Department of Rheumatology & Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Mengmeng Cui
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Xiubin Li
- Department of Neurology, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong Province, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, China
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42
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Liu G, Chen X, Luan Y, Li D. VirusPredictor: XGBoost-based software to predict virus-related sequences in human data. Bioinformatics 2024; 40:btae192. [PMID: 38597887 PMCID: PMC11052659 DOI: 10.1093/bioinformatics/btae192] [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: 10/12/2023] [Revised: 02/29/2024] [Accepted: 04/08/2024] [Indexed: 04/11/2024] Open
Abstract
MOTIVATION Discovering disease causative pathogens, particularly viruses without reference genomes, poses a technical challenge as they are often unidentifiable through sequence alignment. Machine learning prediction of patient high-throughput sequences unmappable to human and pathogen genomes may reveal sequences originating from uncharacterized viruses. Currently, there is a lack of software specifically designed for accurately predicting such viral sequences in human data. RESULTS We developed a fast XGBoost method and software VirusPredictor leveraging an in-house viral genome database. Our two-step XGBoost models first classify each query sequence into one of three groups: infectious virus, endogenous retrovirus (ERV) or non-ERV human. The prediction accuracies increased as the sequences became longer, i.e. 0.76, 0.93, and 0.98 for 150-350 (Illumina short reads), 850-950 (Sanger sequencing data), and 2000-5000 bp sequences, respectively. Then, sequences predicted to be from infectious viruses are further classified into one of six virus taxonomic subgroups, and the accuracies increased from 0.92 to >0.98 when query sequences increased from 150-350 to >850 bp. The results suggest that Illumina short reads should be de novo assembled into contigs (e.g. ∼1000 bp or longer) before prediction whenever possible. We applied VirusPredictor to multiple real genomic and metagenomic datasets and obtained high accuracies. VirusPredictor, a user-friendly open-source Python software, is useful for predicting the origins of patients' unmappable sequences. This study is the first to classify ERVs in infectious viral sequence prediction. This is also the first study combining virus sub-group predictions. AVAILABILITY AND IMPLEMENTATION www.dllab.org/software/VirusPredictor.html.
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Affiliation(s)
- Guangchen Liu
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, United States
- School of Mathematics, Shandong University, Jinan, Shandong 250100, China
- School of Mathematics and Statistics, Ludong University, Yantai, Shandong 264025, China
| | - Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, United States
| | - Yihui Luan
- School of Mathematics, Shandong University, Jinan, Shandong 250100, China
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, United States
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
- ICanCME Research Network, Sainte-Justine University Hospital Research Center, Montreal, Quebec H3T 1C5, Canada
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43
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Schmidtke DT, Hickey AS, Liachko I, Sherlock G, Bhatt AS. Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585998. [PMID: 38562748 PMCID: PMC10983915 DOI: 10.1101/2024.03.20.585998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The prototypic crAssphage (Carjivirus communis) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain its widespread success. Through genomic analyses and culturing, we find that crAssphage uses a phage-plasmid lifestyle to persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, we use a plaque-free culturing approach to measure crAssphage replication in culture with Phocaeicola vulgatus, Phocaeicola dorei, and Bacteroides stercoris, revealing a broad host range. We demonstrate that crAssphage persists with its hosts in culture without causing major cell lysis events or integrating into host chromosomes. The ability to switch between phage and plasmid lifestyles within a wide range of hosts contributes to the prolific nature of crAssphage in the human gut microbiome.
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Affiliation(s)
- Danica T. Schmidtke
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA, USA
- Senior author
| | - Ami S. Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Division of Hematology), Stanford University, Stanford, CA, USA
- Lead corresponding author
- Senior author
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Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584859. [PMID: 38559015 PMCID: PMC10980044 DOI: 10.1101/2024.03.13.584859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.
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Affiliation(s)
- Dylan G Maghini
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Jakob Wirbel
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Luicer A Ingasia Olubayo
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie Smyth
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Theophilous Mathema
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Carl W Belger
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Solomon SR Choma
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Given R Mashaba
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - Lisa Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ami S Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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45
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Li C, Jin S, Lv O, Wang G, Zhang Y, Li S, Zhang W, Long F, Shen Z, Bai S, Zhaxi D, Kong F, Yan Q, Xiao Z. Comparative analysis of the vaginal bacteriome and virome in healthy women living in high-altitude and sea-level areas. Eur J Med Res 2024; 29:157. [PMID: 38454476 PMCID: PMC10918948 DOI: 10.1186/s40001-023-01391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 03/09/2024] Open
Abstract
The vaginal microbiota plays an important role in the health of the female reproductive tract and is closely associated with various pregnancy outcomes and sexually transmitted diseases. Plenty of internal and external factors have strong influence on the changes in a woman's vaginal microbiome. However, the effect of a high-altitude on female vaginal microbiota has not been described. In this study, we characterized the vaginal bacteriome and virome of 13 and 34 healthy women living in high-altitude and sea-level areas, using whole-metagenome shotgun sequencing of their vaginal mucus samples. The results revealed that the vaginal bacteriomes of high-altitude individuals are featured by a significant increase of species diversity, depletion of Lactobacillus crispatus, and more abundant of some anaerobic bacteria, such as Chlamydia trachomatis, Mageeibacillus indolicus, Dialister micraerophilus, and Sneathia amnii). In addition, the vagina samples of sea-level subjects harbor more Lactobacillus strains, whereas the anaerobic bacteroidetes strains mostly appeared in high-altitude subjects. Identified and assembled 191 virus operational taxonomic units (vOTUs), there were significant differences in the abundance of 107 vOTUs between the two groups. Together, the results of this study raised the understanding of bacteriome and virome in the vagina of women at different elevations, and demonstrated that the vaginal microbiome is related to the high-altitude geographic adaptation.
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Affiliation(s)
- Chaoran Li
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Dalian Medical University, Dalian, 116011, China
| | - Song Jin
- Operating Room, First Affiliated Hospital, Dalian Medical University, Dalian, 116011, China
| | - Oingbo Lv
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Wei Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Fang Long
- Department of Obstetrics and Gynecology, People's Hospital of Naqu, Naqu, Tibet, 852000, China
| | - Zhuowei Shen
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Dalian Medical University, Dalian, 116011, China
| | - Siqi Bai
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Dalian Medical University, Dalian, 116011, China
| | - Duoii Zhaxi
- Institute of High Altitude Medicine, People's Hospital of Naqu, Naqu, Tibet, 852000, China
| | - Fandou Kong
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Dalian Medical University, Dalian, 116011, China.
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Zhen Xiao
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Dalian Medical University, Dalian, 116011, China.
- Department of Obstetrics and Gynecology, People's Hospital of Naqu, Naqu, Tibet, 852000, China.
- Institute of High Altitude Medicine, People's Hospital of Naqu, Naqu, Tibet, 852000, China.
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46
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Zeng S, Almeida A, Li S, Ying J, Wang H, Qu Y, Paul Ross R, Stanton C, Zhou Z, Niu X, Mu D, Wang S. A metagenomic catalog of the early-life human gut virome. Nat Commun 2024; 15:1864. [PMID: 38424077 PMCID: PMC10904392 DOI: 10.1038/s41467-024-45793-z] [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: 06/29/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Early-life human gut microbiome is a pivotal driver of gut homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish the Early-Life Gut Virome (ELGV), a catalog of 160,478 non-redundant DNA and RNA viral sequences from 8130 gut virus-like particles (VLPs) enriched or bulk metagenomes in the first three years of life. By clustering, 82,141 viral species are identified, 68.3% of which are absent in existing databases built mainly from adults, and 64 and 8 viral species based on VLPs-enriched and bulk metagenomes, respectively, exhibit potentials as biomarkers to distinguish infants from adults. With the largest longitudinal population of infants profiled by either VLPs-enriched or bulk metagenomic sequencing, we track the inherent instability and temporal development of the early-life human gut virome, and identify differential viruses associated with multiple clinical factors. The mother-infant shared virome and interactions between gut virome and bacteriome early in life are further expanded. Together, the ELGV catalog provides the most comprehensive and complete metagenomic blueprint of the early-life human gut virome, facilitating the discovery of pediatric disease-virome associations in future.
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Affiliation(s)
- Shuqin Zeng
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Shiping Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Junjie Ying
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Hua Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yi Qu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Zhemin Zhou
- Pasteurien College, Medical College of Soochow University, Soochow University, Suzhou, China
| | - Xiaoyu Niu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Dezhi Mu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Shaopu Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
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47
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Istvan P, Birkeland E, Avershina E, Kværner AS, Bemanian V, Pardini B, Tarallo S, de Vos WM, Rognes T, Berstad P, Rounge TB. Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nat Commun 2024; 15:1791. [PMID: 38424056 PMCID: PMC10904388 DOI: 10.1038/s41467-024-46033-0] [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: 08/25/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.
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Affiliation(s)
- Paula Istvan
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Einar Birkeland
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ekaterina Avershina
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ane S Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Vahid Bemanian
- Pathology Department, Akershus University Hospital, Lørenskog, Norway
| | - Barbara Pardini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Sonia Tarallo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Torbjørn Rognes
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Paula Berstad
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Trine B Rounge
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway.
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
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48
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Kienbeck K, Malfertheiner L, Zelger-Paulus S, Johannsen S, von Mering C, Sigel RKO. Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nat Commun 2024; 15:1559. [PMID: 38378708 PMCID: PMC10879173 DOI: 10.1038/s41467-024-45653-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes - theta ribozymes - potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes - we provide 1753 unique examples - highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3'-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.
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Affiliation(s)
- Kasimir Kienbeck
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland
| | | | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland.
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49
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Spohr P, Scharf S, Rommerskirchen A, Henrich B, Jäger P, Klau GW, Haas R, Dilthey A, Pfeffer K. Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing. Sci Rep 2024; 14:4068. [PMID: 38374282 PMCID: PMC10876974 DOI: 10.1038/s41598-024-53506-1] [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: 08/23/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.
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Affiliation(s)
- Philipp Spohr
- Chair Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Düsseldorf, Germany
| | - Sebastian Scharf
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Anna Rommerskirchen
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Paul Jäger
- Department of Hematology, Immunology, and Clinical Immunology, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Gunnar W Klau
- Chair Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Center for Digital Medicine, Düsseldorf, Germany.
| | - Rainer Haas
- Department of Hematology, Immunology, and Clinical Immunology, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
- Center for Digital Medicine, Düsseldorf, Germany.
| | - Klaus Pfeffer
- Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, University Hospital Düsseldorf, Düsseldorf, Germany.
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50
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Shkoporov AN, O'Regan O, Smith L, Khokhlova EV, Draper LA, Ross RP, Hill C. Dynamic nature of viral and bacterial communities in human faeces. iScience 2024; 27:108778. [PMID: 38292428 PMCID: PMC10825054 DOI: 10.1016/j.isci.2023.108778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/20/2023] [Accepted: 12/22/2023] [Indexed: 02/01/2024] Open
Abstract
Bacteriophages are a major component of the gut microbiome and are believed to play a role in establishment and stabilization of microbial communities by influencing taxonomic and functional diversity. We show that the activity of lytic and temperate phages can also significantly affect bacterial community structure in a model of extended colonic retention. Intact fresh human feces were incubated anaerobically at 37°C without homogenization and subjected to metagenomic sequencing. We observed subject-specific blooms and collapses of selected bacteriophage and bacterial populations within some individuals. Most notable were striking collapses of Prevotella populations accompanied by increases in specific bacteriophages. In a number of cases, we even observed a shift from one bacterial "enterotype" to another within 48 h. These results confirm that intact feces represents a highly dynamic ecological system and suggests that colonic retention time could have a profound effect on microbiome composition, including a significant impact by bacteriophages.
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Affiliation(s)
- Andrey N. Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Orla O'Regan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Linda Smith
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | | | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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