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Enav H, Paz I, Ley RE. Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. Nat Biotechnol 2024:10.1038/s41587-024-02276-2. [PMID: 38898177 DOI: 10.1038/s41587-024-02276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/10/2024] [Indexed: 06/21/2024]
Abstract
Microbial species diversify into strains through single-nucleotide mutations and structural changes, such as recombination, insertions and deletions. Most strain-comparison methods quantify differences in single-nucleotide polymorphisms (SNPs) and are insensitive to structural changes. However, recombination is an important driver of phenotypic diversification in many species, including human pathogens. We introduce SynTracker, a tool that compares microbial strains using genome synteny-the order of sequence blocks in homologous genomic regions-in pairs of metagenomic assemblies or genomes. Genome synteny is a rich source of genomic information untapped by current strain-comparison tools. SynTracker has low sensitivity to SNPs, has no database requirement and is robust to sequencing errors. It outperforms existing tools when tracking strains in metagenomic data and is particularly suited for phages, plasmids and other low-data contexts. Applied to single-species datasets and human gut metagenomes, SynTracker, combined with an SNP-based tool, detects strains enriched in either point mutations or structural changes, providing insights into microbial evolution in situ.
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Affiliation(s)
- Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Inbal Paz
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany.
- Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infections (CMFI), University of Tübingen, Tübingen, Germany.
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2
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Li X, Brejnrod A, Trivedi U, Russel J, Thorsen J, Shah SA, Vestergaard GA, Rasmussen MA, Nesme J, Bisgaard H, Stokholm J, Sørensen SJ. Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition. MICROBIOME 2024; 12:87. [PMID: 38730321 PMCID: PMC11084089 DOI: 10.1186/s40168-024-01800-5] [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: 11/21/2023] [Accepted: 03/25/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age. RESULTS We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs. CONCLUSIONS We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.
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Affiliation(s)
- Xuanji Li
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Asker Brejnrod
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Shiraz A Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Gisle Alberg Vestergaard
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Morten Arendt Rasmussen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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3
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Younge N. Influence of infant microbiome on health and development. Clin Exp Pediatr 2024; 67:224-231. [PMID: 37605538 PMCID: PMC11065641 DOI: 10.3345/cep.2023.00598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/08/2023] [Accepted: 07/19/2023] [Indexed: 08/23/2023] Open
Abstract
The microbiome is a complex ecosystem comprising microbes, their genomes, and the surrounding environment. The microbiome plays a critical role in early human development, including maturation of the host immune system and gastrointestinal tract. Multiple factors, including diet, anti-biotic use, and other environmental exposures, influence the establishment of the microbiome during infancy. Numerous studies have identified associations between the microbiome and neonatal diseases, including necrotizing enterocolitis, sepsis, and malnutrition. Furthermore, there is compelling evidence that perturbation of the microbiome in early life can have lasting developmental effects that increase an individual's risk for immune and metabolic diseases in later life. Supplementation of the microbiome with probiotics reduces the risk of necrotizing enterocolitis and sepsis in at-risk infants. This review focuses on the structure and function of the infant microbiome, the environmental and clinical factors that influence its assembly, and its impact on infant health and development.
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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5
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Wei X, Tsai MS, Liang L, Jiang L, Hung CJ, Jelliffe-Pawlowski L, Rand L, Snyder M, Jiang C. Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process. Cell Rep 2024; 43:114078. [PMID: 38598334 DOI: 10.1016/j.celrep.2024.114078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 03/01/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.
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Affiliation(s)
- Xin Wei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Ming-Shian Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liang Liang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Liuyiqi Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Chia-Jui Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Informatics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura Jelliffe-Pawlowski
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Larry Rand
- Department of Obstetrics, Gynecology & Reproductive Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China.
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6
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Xu X, Feng Q, Zhang T, Gao Y, Cheng Q, Zhang W, Wu Q, Xu K, Li Y, Nguyen N, Taft DH, Mills DA, Lemay DG, Zhu W, Mao S, Zhang A, Xu K, Liu J. Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. IMETA 2024; 3:e169. [PMID: 38882494 PMCID: PMC11170968 DOI: 10.1002/imt2.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 06/18/2024]
Abstract
The infant gut microbiome is increasingly recognized as a reservoir of antibiotic resistance genes, yet the assembly of gut resistome in infants and its influencing factors remain largely unknown. We characterized resistome in 4132 metagenomes from 963 infants in six countries and 4285 resistance genes were observed. The inherent resistome pattern of healthy infants (N = 272) could be distinguished by two stages: a multicompound resistance phase (Months 0-7) and a tetracycline-mupirocin-β-lactam-dominant phase (Months 8-14). Microbial taxonomy explained 40.7% of the gut resistome of healthy infants, with Escherichia (25.5%) harboring the most resistance genes. In a further analysis with all available infants (N = 963), we found age was the strongest influencer on the resistome and was negatively correlated with the overall resistance during the first 3 years (p < 0.001). Using a random-forest approach, a set of 34 resistance genes could be used to predict age (R 2 = 68.0%). Leveraging microbial host inference analyses, we inferred the age-dependent assembly of infant resistome was a result of shifts in the gut microbiome, primarily driven by changes in taxa that disproportionately harbor resistance genes across taxa (e.g., Escherichia coli more frequently harbored resistance genes than other taxa). We performed metagenomic functional profiling and metagenomic assembled genome analyses whose results indicate that the development of gut resistome was driven by changes in microbial carbohydrate metabolism, with an increasing need for carbohydrate-active enzymes from Bacteroidota and a decreasing need for Pseudomonadota during infancy. Importantly, we observed increased acquired resistance genes over time, which was related to increased horizontal gene transfer in the developing infant gut microbiome. In summary, infant age was negatively correlated with antimicrobial resistance gene levels, reflecting a composition shift in the gut microbiome, likely driven by the changing need for microbial carbohydrate metabolism during early life.
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Affiliation(s)
- Xinming Xu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Department of Nutrition and Food Hygiene, School of Public Health, Institute of Nutrition Fudan University Shanghai China
| | - Qingying Feng
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
- Biological Engineering Division Massachusetts Institute of Technology (MIT) Cambridge Massachusetts USA
| | - Tao Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Yunlong Gao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qu Cheng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wanqiu Zhang
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Qinglong Wu
- Department of Pathology and Immunology Baylor College of Medicine Houston Texas USA
| | - Ke Xu
- Department of Statistics University of Chicago Chicago Illinois
| | - Yucan Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute Fudan University Shanghai China
| | - Nhu Nguyen
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - Diana H Taft
- Department of Food Science and Technology University of California, Davis Davis California USA
| | - David A Mills
- Department of Food Science and Technology University of California, Davis Davis California USA
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science University of California, Davis Davis California USA
| | - Danielle G Lemay
- USDA ARS Western Human Nutrition Research Center Davis California USA
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences Sichuan University Chengdu China
| | - Kelin Xu
- Department of Biostatistics, Key Laboratory of Public Health Safety, NHC Key Laboratory of Health Technology Assessment, School of Public Health Fudan University Shanghai China
| | - Jinxin Liu
- Laboratory of Gastrointestinal Microbiology, College of Animal Science & Technology Nanjing Agricultural University Nanjing China
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition Nanjing Agricultural University Nanjing China
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7
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Garmaeva S, Sinha T, Gulyaeva A, Kuzub N, Spreckels JE, Andreu-Sánchez S, Gacesa R, Vich Vila A, Brushett S, Kruk M, Dekens J, Sikkema J, Kuipers F, Shkoporov AN, Hill C, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Transmission and dynamics of mother-infant gut viruses during pregnancy and early life. Nat Commun 2024; 15:1945. [PMID: 38431663 PMCID: PMC10908809 DOI: 10.1038/s41467-024-45257-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/16/2024] [Indexed: 03/05/2024] Open
Abstract
Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. To study the development of the infant gut virome over time and the factors that shape it, we longitudinally assess the composition of gut viruses and their bacterial hosts in 30 women during and after pregnancy and in their 32 infants during their first year of life. Using shotgun metagenomic sequencing applied to dsDNA extracted from Virus-Like Particles (VLPs) and bacteria, we generate 205 VLP metaviromes and 322 total metagenomes. With this data, we show that while the maternal gut virome composition remains stable during late pregnancy and after birth, the infant gut virome is dynamic in the first year of life. Notably, infant gut viromes contain a higher abundance of active temperate phages compared to maternal gut viromes, which decreases over the first year of life. Moreover, we show that the feeding mode and place of delivery influence the gut virome composition of infants. Lastly, we provide evidence of co-transmission of viral and bacterial strains from mothers to infants, demonstrating that infants acquire some of their virome from their mother's gut.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nataliia Kuzub
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johanne E Spreckels
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Siobhan Brushett
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jackie Dekens
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University Medical Center Groningen, Center for Development and Innovation, Groningen, Netherlands
| | - Jan Sikkema
- University Medical Center Groningen, Center for Development and Innovation, Groningen, Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Andrey N Shkoporov
- 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
| | - Sicco Scherjon
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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8
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Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM. A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell 2024; 187:1206-1222.e16. [PMID: 38428395 DOI: 10.1016/j.cell.2024.01.039] [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: 03/29/2023] [Revised: 10/03/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.
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Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry, University of Chicago, Chicago, IL 60637, USA
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Laurie E Comstock
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany; Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany.
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9
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Zhang L, Agrawal M, Ng SC, Jess T. Early-life exposures and the microbiome: implications for IBD prevention. Gut 2024; 73:541-549. [PMID: 38123972 PMCID: PMC11150004 DOI: 10.1136/gutjnl-2023-330002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
The early-life period is one of microbiome establishment and immune maturation. Early-life exposures are increasingly being recognised to play an important role in IBD risk. The composition of functions of the gut microbiome in the prenatal, perinatal, and postnatal period may be crucial towards development of health or disease, including IBD, later in life. We herein present a comprehensive summary of the interplay between early-life factors and microbiome perturbations, and their association with risk of IBD. In addition, we provide an overview of host and external factors in early life that are known to impact gut microbiome maturation and exposures implicated in IBD risk. Considering the emerging concept of IBD prevention, we propose strategies to minimise maternal and offspring exposure to potentially harmful variables and recommend protective measures during pregnancy and the postpartum period. This holistic view of early-life factors and microbiome signatures among mothers and their offspring will help frame our current understanding of their importance towards IBD pathogenesis and frame the roadmap for preventive strategies.
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Affiliation(s)
- Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Manasi Agrawal
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York NY, New York, USA
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease (PREDICT), Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Gastroenterology & Hepatology, Aalborg University Hospital, Aalborg, Denmark
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10
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Patangia DV, Grimaud G, O'Shea CA, Ryan CA, Dempsey E, Stanton C, Ross RP. Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome. MICROBIOME 2024; 12:19. [PMID: 38310316 PMCID: PMC10837951 DOI: 10.1186/s40168-023-01732-6] [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: 05/09/2023] [Accepted: 11/24/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied. METHODS Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort's first week of life. RESULTS Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs). CONCLUSION These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures-leading to what can be an extensive and diverse resistome. Video Abstract.
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Affiliation(s)
- Dhrati V Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | | | - C A Ryan
- APC Microbiome Ireland, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- Infant Research Centre, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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11
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Baker JS, Qu E, Mancuso CP, Tripp AD, Conwill A, Lieberman TD. Highly-resolved within-species dynamics in the human facial skin microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575018. [PMID: 38260404 PMCID: PMC10802602 DOI: 10.1101/2024.01.10.575018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Human facial skin microbiomes (FSMs) on adults are dominated by just two bacterial species, Cutibacterium acnes and Staphylococcus epidermidis. Underlying this apparent simplicity, each FSM harbors multiple strains of both species whose assembly dynamics on individuals are unknown. Here, we use 4,055 isolate genomes and 360 metagenomes to trace the dynamics of strains on individuals and their transmission. Strains are shared amongst family members of all ages, but each individual harbors unique strain consortia. Strain stability changes upon formation of the adult-type FSM: S. epidermidis lineage turnover slows, and the rate of C. acnes colonization increases before stabilizing, suggesting this transitional window could facilitate engraftment of therapeutic strains. Our work reveals previously undetectable community dynamics and informs the design of therapeutic interventions.
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Affiliation(s)
- Jacob S. Baker
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Evan Qu
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Christopher P. Mancuso
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - A. Delphine Tripp
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Systems Biology, Harvard University; Cambridge, MA 02138, USA
| | - Arolyn Conwill
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Tami D. Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA 02139, USA
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12
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Minot SS, Mayer-Blackwell K, Fiore-Gartland A, Johnson A, Self S, Bhatti P, Yao L, Liu L, Sun X, Jinfa Y, Kublin J. Strain-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.16.23300077. [PMID: 38168439 PMCID: PMC10760300 DOI: 10.1101/2023.12.16.23300077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background The human gut microbiome develops rapidly during infancy, a key window of development coinciding with maturation of the adaptive immune system. However, little is known of the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n=94) from a cohort of infants (n=15) at monthly intervals in the first six months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants. Results Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual. Conclusion By augmenting published metagenomic datasets with data from a newly established cohort we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.
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Affiliation(s)
| | | | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Andrew Johnson
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Steven Self
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Parveen Bhatti
- Cancer Control Research, BC Cancer Research Institute, Vancouver, BC, Canada
- Epidemiology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Lena Yao
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Lili Liu
- Key Laboratory of Occupational Disease Prevention and Treatment, Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, China
| | - Xin Sun
- National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jinfa
- Nanhai Maternity and Child Healthcare Hospital of Foshan, Foshan, China
| | - James Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
- HIV Vaccine Trials Network, Fred Hutchinson Cancer Center, Seattle, USA
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13
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Baud GLC, Prasad A, Ellegaard KM, Engel P. Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers. Genome Biol 2023; 24:283. [PMID: 38066630 PMCID: PMC10704631 DOI: 10.1186/s13059-023-03131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood. RESULTS Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states. CONCLUSIONS Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.
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Affiliation(s)
- Gilles L C Baud
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Aiswarya Prasad
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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14
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Austin GI, Park H, Meydan Y, Seeram D, Sezin T, Lou YC, Firek BA, Morowitz MJ, Banfield JF, Christiano AM, Pe'er I, Uhlemann AC, Shenhav L, Korem T. Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. Nat Biotechnol 2023; 41:1820-1828. [PMID: 36928429 PMCID: PMC10504420 DOI: 10.1038/s41587-023-01696-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 01/23/2023] [Indexed: 03/18/2023]
Abstract
Sequencing-based approaches for the analysis of microbial communities are susceptible to contamination, which could mask biological signals or generate artifactual ones. Methods for in silico decontamination using controls are routinely used, but do not make optimal use of information shared across samples and cannot handle taxa that only partially originate in contamination or leakage of biological material into controls. Here we present Source tracking for Contamination Removal in microBiomes (SCRuB), a probabilistic in silico decontamination method that incorporates shared information across multiple samples and controls to precisely identify and remove contamination. We validate the accuracy of SCRuB in multiple data-driven simulations and experiments, including induced contamination, and demonstrate that it outperforms state-of-the-art methods by an average of 15-20 times. We showcase the robustness of SCRuB across multiple ecosystems, data types and sequencing depths. Demonstrating its applicability to microbiome research, SCRuB facilitates improved predictions of host phenotypes, most notably the prediction of treatment response in melanoma patients using decontaminated tumor microbiome data.
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Affiliation(s)
- George I Austin
- Department of Computer Science, Columbia University, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Yoli Meydan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Dwayne Seeram
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Tanya Sezin
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Angela M Christiano
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA.
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada.
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15
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Lou YC, Rubin BE, Schoelmerich MC, DiMarco KS, Borges AL, Rovinsky R, Song L, Doudna JA, Banfield JF. Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species. Nat Commun 2023; 14:7417. [PMID: 37973815 PMCID: PMC10654741 DOI: 10.1038/s41467-023-43279-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2'-fucosyllactose (2'FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2'FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2'FL breakdown, thus critical for B. breve's growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2'FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual's microbiome.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland
| | - Kaden S DiMarco
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Leo Song
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
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16
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Heston SM, Lim CSE, Ong C, Chua MC, Kelly MS, Yeo KT. Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore. Gut Pathog 2023; 15:55. [PMID: 37974294 PMCID: PMC10652614 DOI: 10.1186/s13099-023-00583-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Gut dysbiosis contributes to the high risk of bloodstream infection (BSI) among premature infants. Most prior studies of the premature infant gut microbiota were conducted in Western countries and prior to development of current tools for strain-resolved analysis. METHODS We performed metagenomic sequencing of weekly fecal samples from 75 premature infants at a single hospital in Singapore. We evaluated associations between clinical factors and gut microbiota composition using PERMANOVA and mixed effects linear regression. We used inStrain to perform strain-level analyses evaluating for gut colonization by BSI-causing strains. RESULTS Median (interquartile range) gestation was 27 (25, 29) weeks, and 63% of infants were born via Cesarean section. Antibiotic exposures (PERMANOVA; R2 = 0.017, p = 0.001) and postnatal age (R2 = 0.015, p = 0.001) accounted for the largest amount of variability in gut microbiota composition. Increasing postnatal age was associated with higher relative abundances of several common pathogens (Enterococcus faecalis: p < 0.0001; Escherichia coli: p < 0.0001; Klebsiella aerogenes: p < 0.0001; Klebsiella pneumoniae: p < 0.0001). Antibiotic exposures were generally associated with lower relative abundances of both frequently beneficial bacteria (e.g., Bifidobacterium species) and common enteric pathogens (e.g., Enterobacter, Klebsiella species). We identified strains identical to the blood culture isolate in fecal samples from 12 of 16 (75%) infants who developed BSI, including all infections caused by typical enteric bacteria. CONCLUSIONS Antibiotic exposures were the dominant modifiable factor affecting gut microbiota composition in a large cohort of premature infants from South-East Asia. Strain-resolved analyses indicate that the gut is an important reservoir for organisms causing BSI among premature infants.
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Affiliation(s)
- Sarah M Heston
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Charis Shu En Lim
- Department of Neonatology, KK Women's and Children's Hospital, Singapore, Singapore
| | - Chengsi Ong
- Department of Neonatology, KK Women's and Children's Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Nutrition and Dietetics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Mei Chien Chua
- Department of Neonatology, KK Women's and Children's Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Matthew S Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Kee Thai Yeo
- Department of Neonatology, KK Women's and Children's Hospital, Singapore, Singapore.
- Duke-NUS Medical School, Singapore, Singapore.
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17
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Thurimella K, Mohamed AMT, Graham DB, Owens RM, La Rosa SL, Plichta DR, Bacallado S, Xavier RJ. Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563620. [PMID: 37961379 PMCID: PMC10634757 DOI: 10.1101/2023.10.23.563620] [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
In metagenomics, the pool of uncharacterized microbial enzymes presents a challenge for functional annotation. Among these, carbohydrate-active enzymes (CAZymes) stand out due to their pivotal roles in various biological processes related to host health and nutrition. Here, we present CAZyLingua, the first tool that harnesses protein language model embeddings to build a deep learning framework that facilitates the annotation of CAZymes in metagenomic datasets. Our benchmarking results showed on average a higher F1 score (reflecting an average of precision and recall) on the annotated genomes of Bacteroides thetaiotaomicron, Eggerthella lenta and Ruminococcus gnavus compared to the traditional sequence homology-based method in dbCAN2. We applied our tool to a paired mother/infant longitudinal dataset and revealed unannotated CAZymes linked to microbial development during infancy. When applied to metagenomic datasets derived from patients affected by fibrosis-prone diseases such as Crohn's disease and IgG4-related disease, CAZyLingua uncovered CAZymes associated with disease and healthy states. In each of these metagenomic catalogs, CAZyLingua discovered new annotations that were previously overlooked by traditional sequence homology tools. Overall, the deep learning model CAZyLingua can be applied in combination with existing tools to unravel intricate CAZyme evolutionary profiles and patterns, contributing to a more comprehensive understanding of microbial metabolic dynamics.
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Affiliation(s)
- Kumar Thurimella
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ahmed M. T. Mohamed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel B. Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Róisín M. Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Damian R. Plichta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergio Bacallado
- Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, UK
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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18
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Abstract
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Cindy J Castelle
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
| | - Jillian F Banfield
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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19
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Buzun E, Hsu CY, Sejane K, Oles RE, Ayala AV, Loomis LR, Zhao J, Rossitto LA, McGrosso D, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early life colonization by a pioneering gut commensal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552477. [PMID: 37609270 PMCID: PMC10441351 DOI: 10.1101/2023.08.08.552477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The early microbial colonization of the gastrointestinal tract can lead to long-term impacts in development and overall human health. Keystone species, including Bacteroides spp ., play a crucial role in maintaining the structure, diversity, and function of the intestinal ecosystem. However, the process by which a defined and resilient community is curated and maintained during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa and regulates the commensal colonization program during the first weeks of life. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. After examining the dynamics between pioneer gut Bacteroides species in the murine gut, we discovered that NanH enables vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, we demonstrate that NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and the microbiota mediated through host-derived glycans to promote stable intestinal colonization.
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20
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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Lee STM. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome 2023; 5:35. [PMID: 37461084 DOI: 10.1186/s42523-023-00256-6] [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: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. RESULTS We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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21
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Wu J, Zhang H, Gan R, Xia Y, Zhang F, Wang D, Fu J, Barraclough TG. CRISPR dynamics during the interaction between bacteria and phage in the first year of life. Microb Genom 2023; 9:mgen001053. [PMID: 37402176 PMCID: PMC10438810 DOI: 10.1099/mgen.0.001053] [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: 11/22/2022] [Accepted: 05/26/2023] [Indexed: 07/06/2023] Open
Abstract
Gut microbiomes in infancy have a profound impact on health in adulthood. CRISPRs play an essential role in the interaction between bacteria and phages. However, the dynamics of CRISPRs in gut microbiomes during early life are poorly understood. In this study, using shotgun metagenomic sequencing data from 82 Swedish infants' gut microbiomes, 1882 candidate CRISPRs were identified, and their dynamics were analysed. We found large-scale turnover of CRISPRs and their spacers during the first year of life. As well as changes in relative abundance of the bacteria containing CRISPR, acquisition, loss and mutation of spacers were observed within the same CRISPR array sampled over time. Accordingly, the inferred interaction network of bacteria and phage was distinct at different times. This research underpins CRISPR dynamics and their potential role in the interaction between bacteria and phage in early life.
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Affiliation(s)
- Jiqiu Wu
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- West China Biomedical Big Data Center, West China Hospital/West China School of Medicine, Sichuan University, Chengdu 610041, PR China
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, Netherlands
| | - Hanyun Zhang
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Rui Gan
- Changping Laboratory, Beijing 102206, PR China
| | - Yan Xia
- 01Life Institute, Shenzhen 518000, PR China
| | - Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, PR China
| | - Daoming Wang
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9713 AV, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, Netherlands
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, UK
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22
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Sharon BM, Hulyalkar NV, Zimmern PE, Palmer KL, De Nisco NJ. Inter-species diversity and functional genomic analyses of closed genome assemblies of clinically isolated, megaplasmid-containing Enterococcus raffinosus Er676 and ATCC49464. Access Microbiol 2023; 5:acmi000508.v3. [PMID: 37424546 PMCID: PMC10323788 DOI: 10.1099/acmi.0.000508.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/10/2023] [Indexed: 07/11/2023] Open
Abstract
Enterococcus raffinosus is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human infection compared to other enterococci, this species can cause disease and persist in diverse niches such as the gut, urinary tract, blood and environment. Few complete genome assemblies have been published to date for E. raffinosus . In this study, we report the complete assembly of the first clinical urinary E. raffinosus strain, Er676, isolated from a postmenopausal woman with history of recurrent urinary tract infection. We additionally completed the assembly of clinical type strain ATCC49464. Comparative genomic analyses reveal inter-species diversity driven by large accessory genomes. The presence of a conserved megaplasmid indicates it is a ubiquitous and vital genetic feature of E. raffinosus . We find that the E. raffinosus chromosome is enriched for DNA replication and protein biosynthesis genes while the megaplasmid is enriched for transcription and carbohydrate metabolism genes. Prophage analysis suggests that diversity in the chromosome and megaplasmid sequences arises, in part, from horizontal gene transfer. Er676 demonstrated the largest genome size reported to date for E. raffinosus and the highest probability of human pathogenicity. Er676 also possesses multiple antimicrobial resistance genes, of which all but one are encoded on the chromosome, and has the most complete prophage sequences. Complete assembly and comparative analyses of the Er676 and ATCC49464 genomes provide important insight into the inter-species diversity of E. raffinosus that gives it its ability to colonize and persist in the human body. Investigating genetic factors that contribute to the pathogenicity of this species will provide valuable tools to combat diseases caused by this opportunistic pathogen.
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Affiliation(s)
- Belle M. Sharon
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Neha V. Hulyalkar
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
| | - Nicole J. De Nisco
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas, USA
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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23
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Feehily C, O'Neill IJ, Walsh CJ, Moore RL, Killeen SL, Geraghty AA, Lawton EM, Byrne D, Sanchez-Gallardo R, Nori SRC, Nielsen IB, Wortmann E, Matthews E, O'Flaherty R, Rudd PM, Groeger D, Shanahan F, Saldova R, McAuliffe FM, Van Sinderen D, Cotter PD. Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach. Nat Commun 2023; 14:3015. [PMID: 37230981 DOI: 10.1038/s41467-023-38694-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.
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Affiliation(s)
- Conor Feehily
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
| | - Ian J O'Neill
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
| | - Rebecca L Moore
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Sarah Louise Killeen
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Aisling A Geraghty
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Elaine M Lawton
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
| | - David Byrne
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Rocio Sanchez-Gallardo
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Sai Ravi Chandra Nori
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, School of Mathematics, Statistics & Applied Mathematics, University of Galway, Galway, Ireland
| | - Ida Busch Nielsen
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Esther Wortmann
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Elizabeth Matthews
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
| | - Roisin O'Flaherty
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
- Department of Chemistry, Maynooth University, Maynooth, Co, Kildare, Ireland
| | - Pauline M Rudd
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
- Bioprocessing Technology Institute, AStar, Singapore, Singapore
| | - David Groeger
- PrecisionBiotics Group Ltd. (Novozymes Cork), Cork Airport Business Park, Kinsale Road, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
| | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research and Training, Co, Dublin, Ireland
- UCD School of Medicine, College of Health and Agricultural Science (CHAS), University College Dublin (UCD), Dublin, Ireland
| | - Fionnuala M McAuliffe
- UCD Perinatal Research Centre, School of Medicine, University College Dublin, National Maternity Hospital, Dublin, Ireland
| | - Douwe Van Sinderen
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Co, Cork, Ireland
- APC Microbiome Ireland, National University of Ireland, Cork, Ireland
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24
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Prasad A, Ene A, Jablonska S, Du J, Wolfe AJ, Putonti C. Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains. mSphere 2023; 8:e0068722. [PMID: 36744899 PMCID: PMC10117062 DOI: 10.1128/msphere.00687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.
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Affiliation(s)
- Ananya Prasad
- School of Biological Sciences, University of California San Diego, San Diego, California, USA
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Sandra Jablonska
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Jingjie Du
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
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25
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Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore R, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Mclellan SL, Willis AD, Comstock LE, Eren AM. A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534219. [PMID: 36993556 PMCID: PMC10055365 DOI: 10.1101/2023.03.25.534219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.
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Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L. Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY, 10032 USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry, University of Chicago, Chicago, IL, 60637, USA
| | | | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Laurie E Comstock
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
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26
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Lou YC, Hoff J, Olm MR, West-Roberts J, Diamond S, Firek BA, Morowitz MJ, Banfield JF. Using strain-resolved analysis to identify contamination in metagenomics data. MICROBIOME 2023; 11:36. [PMID: 36864482 PMCID: PMC9979413 DOI: 10.1186/s40168-023-01477-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 01/28/2023] [Indexed: 05/06/2023]
Abstract
BACKGROUND Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported. RESULTS Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass. CONCLUSION Our work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls. Video Abstract.
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Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jordan Hoff
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
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27
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Tian M, Li Q, Zheng T, Yang S, Chen F, Guan W, Zhang S. Maternal microbe-specific modulation of the offspring microbiome and development during pregnancy and lactation. Gut Microbes 2023; 15:2206505. [PMID: 37184203 DOI: 10.1080/19490976.2023.2206505] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The maternal microbiome is essential for the healthy growth and development of offspring and has long-term effects later in life. Recent advances indicate that the maternal microbiome begins to regulate fetal health and development during pregnancy. Furthermore, the maternal microbiome continues to affect early microbial colonization via birth and breastfeeding. Compelling evidence indicates that the maternal microbiome is involved in the regulation of immune and brain development and affects the risk of related diseases. Modulating offspring development by maternal diet and probiotic intervention during pregnancy and breastfeeding could be a promising therapy in the future. In this review, we summarize and discuss the current understanding of maternal microbiota development, perinatal microbial metabolite transfer, mother-to-infant microbial transmission during/after birth and its association with immune and brain development as well as corresponding diseases.
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Affiliation(s)
- Min Tian
- Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Qihui Li
- Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Tenghui Zheng
- Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Siwang Yang
- Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Fang Chen
- Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Wutai Guan
- Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Shihai Zhang
- Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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28
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Yilmaz B, Fuhrer T, Morgenthaler D, Krupka N, Wang D, Spari D, Candinas D, Misselwitz B, Beldi G, Sauer U, Macpherson AJ. Plasticity of the adult human small intestinal stoma microbiota. Cell Host Microbe 2022; 30:1773-1787.e6. [PMID: 36318918 DOI: 10.1016/j.chom.2022.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022]
Abstract
The human distal small intestine (ileum) has a distinct microbiota, but human studies investigating its composition and function have been limited by the inaccessibility of the ileum without purging and/or deep intubation. We investigated inherent instability, temporal dynamics, and the contribution of fed and fasted states using stoma samples from cured colorectal cancer patients as a non-invasive access route to the otherwise inaccessible small and large intestines. Sequential sampling of the ileum before and after stoma formation indicated that ileostoma microbiotas represented that of the intact small intestine. Ileal and colonic stoma microbiotas were confirmed as distinct, and two types of instability in ileal host-microbial relationships were observed: inter-digestive purging followed by the rapid postprandial blooming of bacterial biomass and sub-strain appearance and disappearance within individual taxa after feeding. In contrast to the relative stability of colonic microbiota, the human small intestinal microbiota biomass and its sub-strain composition can be highly dynamic.
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Affiliation(s)
- Bahtiyar Yilmaz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3008 Bern, Switzerland.
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Deborah Morgenthaler
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Niklas Krupka
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Daniel Spari
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Daniel Candinas
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Benjamin Misselwitz
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Guido Beldi
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Andrew J Macpherson
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, 3008 Bern, Switzerland.
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29
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Human Milk Microbiome and Microbiome-Related Products: Potential Modulators of Infant Growth. Nutrients 2022; 14:nu14235148. [PMID: 36501178 PMCID: PMC9737635 DOI: 10.3390/nu14235148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Infant growth trajectory may influence later-life obesity. Human milk provides a wide range of nutritional and bioactive components that are vital for infant growth. Compared to formula-fed infants, breastfed infants are less likely to develop later-onset obesity, highlighting the potential role of bioactive components present in human milk. Components of particular interest are the human milk microbiota, human milk oligosaccharides (HMOs), short-chain fatty acids (SCFAs), and antimicrobial proteins, each of which influence the infant gut microbiome, which in turn has been associated with infant body composition. SCFAs and antimicrobial proteins from human milk may also systemically influence infant metabolism. Although inconsistent, multiple studies have reported associations between HMOs and infant growth, while studies on other bioactive components in relation to infant growth are sparse. Moreover, these microbiome-related components may interact with each other within the mammary gland. Here, we review the evidence around the impact of human milk microbes, HMOs, SCFAs, and antimicrobial proteins on infant growth. Breastfeeding is a unique window of opportunity to promote optimal infant growth, with aberrant growth trajectories potentially creating short- and long-term public health burdens. Therefore, it is important to understand how bioactive components of human milk influence infant growth.
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30
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Matharu D, Ponsero AJ, Dikareva E, Korpela K, Kolho KL, de Vos WM, Salonen A. Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories. Front Microbiol 2022; 13:953475. [PMID: 36274732 PMCID: PMC9583133 DOI: 10.3389/fmicb.2022.953475] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background and aims Birth mode and other early life factors affect a newborn's microbial colonization with potential long-term health effects. Individual variations in early life gut microbiota development, especially their effects on the functional repertoire of microbiota, are still poorly characterized. This study aims to provide new insights into the gut microbiome developmental trajectories during the first year of life. Methods Our study comprised 78 term infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 280 total samples), and their mothers were sampled in late pregnancy (n = 50). Fecal DNA was subjected to shotgun metagenomic sequencing. Infant samples were studied for taxonomic and functional maturation, and maternal microbiota was used as a reference. Hierarchical clustering on taxonomic profiles was used to identify the main microbiota developmental trajectories in the infants, and their associations with perinatal and postnatal factors were assessed. Results In line with previous studies, infant microbiota composition showed increased alpha diversity and decreased beta diversity by age, converging toward an adult-like profile. However, we did not observe an increase in functional alpha diversity, which was stable and comparable with the mother samples throughout all the sampling points. Using a de novo clustering approach, two main infant microbiota clusters driven by Bacteroidaceae and Clostridiaceae emerged at each time point. The clusters were associated with birth mode and their functions differed mainly in terms of biosynthetic and carbohydrate degradation pathways, some of which consistently differed between the clusters for all the time points. The longitudinal analysis indicated three main microbiota developmental trajectories, with the majority of the infants retaining their characteristic cluster until 1 year. As many as 40% of vaginally delivered infants were grouped with infants delivered by C-section due to their clear and persistent depletion in Bacteroides. Intrapartum antibiotics, any perinatal or postnatal factors, maternal microbiota composition, or other maternal factors did not explain the depletion in Bacteroides in the subset of vaginally born infants. Conclusion Our study provides an enhanced understanding of the compositional and functional early life gut microbiota trajectories, opening avenues for investigating elusive causes that influence non-typical microbiota development.
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Affiliation(s)
- Dollwin Matharu
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alise J. Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ, United States
| | - Evgenia Dikareva
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children's Hospital, Pediatric Research Center, University of Helsinki and HUS, Helsinki, Finland
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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31
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Peters SL, Borges AL, Giannone RJ, Morowitz MJ, Banfield JF, Hettich RL. Experimental validation that human microbiome phages use alternative genetic coding. Nat Commun 2022; 13:5710. [PMID: 36175428 PMCID: PMC9523058 DOI: 10.1038/s41467-022-32979-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/25/2022] [Indexed: 11/12/2022] Open
Abstract
Previous bioinformatic analyses of metagenomic data have indicated that bacteriophages can use genetic codes different from those of their host bacteria. In particular, reassignment of stop codon TAG to glutamine (a variation known as 'genetic code 15') has been predicted. Here, we use LC-MS/MS-based metaproteomics of human fecal samples to provide experimental evidence of the use of genetic code 15 in two crAss-like phages. Furthermore, the proteomic data from several phage structural proteins supports the reassignment of the TAG stop codon to glutamine late in the phage infection cycle. Thus, our work experimentally validates the expression of genetic code 15 in human microbiome phages.
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Affiliation(s)
- Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | | | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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32
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Mazenc A, Mervant L, Maslo C, Lencina C, Bézirard V, Levêque M, Ahn I, Alquier-Bacquié V, Naud N, Héliès-Toussaint C, Debrauwer L, Chevolleau S, Guéraud F, Pierre FHF, Théodorou V, Olier M. Maternal heme-enriched diet promotes a gut pro-oxidative status associated with microbiota alteration, gut leakiness and glucose intolerance in mice offspring. Redox Biol 2022; 53:102333. [PMID: 35588638 PMCID: PMC9119830 DOI: 10.1016/j.redox.2022.102333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 12/17/2022] Open
Abstract
Maternal environment, including nutrition and microbiota, plays a critical role in determining offspring's risk of chronic diseases such as diabetes later in life. Heme iron requirement is amplified during pregnancy and lactation, while excessive dietary heme iron intake, compared to non-heme iron, has shown to trigger acute oxidative stress in the gut resulting from reactive aldehyde formation in conjunction with microbiota reshape. Given the immaturity of the antioxidant defense system in early life, we investigated the extent to which a maternal diet enriched with heme iron may have a lasting impact on gut homeostasis and glucose metabolism in 60-day-old C3H/HeN mice offspring. As hypothesized, the form of iron added to the maternal diet differentially governed the offspring's microbiota establishment despite identical fecal iron status in the offspring. Importantly, despite female offspring was unaffected, oxidative stress markers were however higher in the gut of male offspring from heme enriched-fed mothers, and were accompanied by increases in fecal lipocalin-2, intestinal para-cellular permeability and TNF-α expression. In addition, male mice displayed blood glucose intolerance resulting from impaired insulin secretion following oral glucose challenge. Using an integrated approach including an aldehydomic analysis, this male-specific phenotype was further characterized and revealed close covariations between unidentified putative reactive aldehydes and bacterial communities belonging to Bacteroidales and Lachnospirales orders. Our work highlights how the form of dietary iron in the maternal diet can dictate the oxidative status in gut offspring in a sex-dependent manner, and how a gut microbiota-driven oxidative challenge in early life can be associated with gut barrier defects and glucose metabolism disorders that may be predictive of diabetes development. Maternal heminic vs. non-heminic iron intake differentially and persistently imprints the offspring's fecal microbiota. Males from heme-fed dams exhibit increased gut lumen reactive aldehydes in absence of direct dietary exposure to heme iron. Some of the increased reactive aldehydes closely covariated with Orders belonging to Bacteroidales and Lachnospirales. Maternal exposure to dietary heme iron impairs gut barrier and glucose tolerance in male offspring.
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Affiliation(s)
- Anaïs Mazenc
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Loïc Mervant
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France; Metatoul-AXIOM Plaform, National Infrastructure for Metabolomics and Fluxomics, MetaboHUB, Toulouse, France
| | - Claire Maslo
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Corinne Lencina
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Valérie Bézirard
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Mathilde Levêque
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Ingrid Ahn
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Valérie Alquier-Bacquié
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Nathalie Naud
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Cécile Héliès-Toussaint
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France; Metatoul-AXIOM Plaform, National Infrastructure for Metabolomics and Fluxomics, MetaboHUB, Toulouse, France
| | - Sylvie Chevolleau
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France; Metatoul-AXIOM Plaform, National Infrastructure for Metabolomics and Fluxomics, MetaboHUB, Toulouse, France
| | - Françoise Guéraud
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Fabrice H F Pierre
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Vassilia Théodorou
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Maïwenn Olier
- Toxalim (Research Centre in Food Toxicology), INRAE, Université de Toulouse, ENVT, INP-Purpan, UPS, Toulouse, France.
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33
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Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng XD, Tripathi S, Wastyk H, Neff N, Holmes S, Sonnenburg ED, Jha AR, Sonnenburg JL. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science 2022; 376:1220-1223. [PMID: 35679413 PMCID: PMC9894631 DOI: 10.1126/science.abj2972] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Infant microbiome assembly has been intensely studied in infants from industrialized nations, but little is known about this process in nonindustrialized populations. We deeply sequenced infant stool samples from the Hadza hunter-gatherers of Tanzania and analyzed them in a global meta-analysis. Infant microbiomes develop along lifestyle-associated trajectories, with more than 20% of genomes detected in the Hadza infant gut representing novel species. Industrialized infants-even those who are breastfed-have microbiomes characterized by a paucity of Bifidobacterium infantis and gene cassettes involved in human milk utilization. Strains within lifestyle-associated taxonomic groups are shared between mother-infant dyads, consistent with early life inheritance of lifestyle-shaped microbiomes. The population-specific differences in infant microbiome composition and function underscore the importance of studying microbiomes from people outside of wealthy, industrialized nations.
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Affiliation(s)
- Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew M. Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan D. Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hannah Wastyk
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Susan Holmes
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Statistics, Stanford University, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Corresponding author:
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34
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Borges AL, Lou YC, Sachdeva R, Al-Shayeb B, Penev PI, Jaffe AL, Lei S, Santini JM, Banfield JF. Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes. Nat Microbiol 2022; 7:918-927. [PMID: 35618772 DOI: 10.1038/s41564-022-01128-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 04/21/2022] [Indexed: 11/09/2022]
Abstract
Bacteriophages (phages) are obligate parasites that use host bacterial translation machinery to produce viral proteins. However, some phages have alternative genetic codes with reassigned stop codons that are predicted to be incompatible with bacterial translation systems. We analysed 9,422 phage genomes and found that stop-codon recoding has evolved in diverse clades of phages that infect bacteria present in both human and animal gut microbiota. Recoded stop codons are particularly over-represented in phage structural and lysis genes. We propose that recoded stop codons might function to prevent premature production of late-stage proteins. Stop-codon recoding has evolved several times in closely related lineages, which suggests that adaptive recoding can occur over very short evolutionary timescales.
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Affiliation(s)
- Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.,Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Yue Clare Lou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.,Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Petar I Penev
- Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Shufei Lei
- Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Joanne M Santini
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA. .,Environmental Science, Policy and Management, University of California, Berkeley, CA, USA. .,Earth and Planetary Science, University of California, Berkeley, CA, USA. .,Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,The University of Melbourne, Parkville, Victoria, Australia.
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35
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Barratt MJ, Ahmed T, Gordon JI. Gut microbiome development and childhood undernutrition. Cell Host Microbe 2022; 30:617-626. [PMID: 35550665 PMCID: PMC9504993 DOI: 10.1016/j.chom.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Forty-five percent of deaths among children under 5 years of age are associated with undernutrition. Globally, almost 200 million children exhibit the two major forms of undernutrition-wasting (low weight-for-height) or stunting (low height-for-age), with many affected by both. Undernutrition is not due to food insecurity alone. Growing evidence indicates that perturbed postnatal gut microbiome development contributes to its pathogenesis. This perspective focuses on defining and repairing these defects in gut microbiome development. We describe an approach that involves the analysis of well-phenotyped human cohorts, followed by preclinical studies using gnotobiotic animals colonized with microbiota from these cohorts. Additionally, these models can be used to identify therapeutic targets and candidates that can then be tested clinically. Furthermore, introducing pretreatment microbiota from trial participants into gnotobiotic animals and re-enacting trial conditions allow mechanisms to be dissected. We highlight these recent advances as well as gaps in existing knowledge that present opportunities for future research.
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Affiliation(s)
- Michael J. Barratt
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63110,Center for Gut Microbiome Research, Washington University in St. Louis, St. Louis, MO 63110
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh
| | - Jeffrey I. Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63110,Center for Gut Microbiome Research, Washington University in St. Louis, St. Louis, MO 63110
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36
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Abstract
At birth, neonates provide a vast habitat awaiting microbial colonization. Microbiome assembly is a complex process involving microbial seeding and succession driven by ecological forces and subject to environmental conditions. These successional events not only significantly affect the ecology and function of the microbiome, but also impact host health. While the establishment of the infant microbiome has been a point of interest for decades, an integrated view focusing on strain level colonization has been lacking until recently. Technological and computational advancements enabling strain-level analyses of the infant microbiome have demonstrated the immense complexity of this system and allowed for an improved understanding of how strains of the same species spread, colonize, evolve, and affect the host. Here, we review the current knowledge of the establishment and maturation of the infant gut microbiome with particular emphasis on newer discoveries achieved through strain-centric analyses.
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Affiliation(s)
- Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
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37
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Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol 2022; 7:34-47. [PMID: 34873292 PMCID: PMC9261505 DOI: 10.1038/s41564-021-01014-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/29/2021] [Indexed: 12/13/2022]
Abstract
Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.
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Affiliation(s)
- Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Spencer Diamond
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Yue Clare Lou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Christine He
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Michael Xu
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Zeyi Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sara J Smith
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Kimberly Tang
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Trenton K Owens
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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