1
|
Xun W, Liu Y, Ma A, Yan H, Miao Y, Shao J, Zhang N, Xu Z, Shen Q, Zhang R. Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture. THE NEW PHYTOLOGIST 2024; 242:2401-2410. [PMID: 38494698 DOI: 10.1111/nph.19697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.
Collapse
Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Aiyuan Ma
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - He Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
2
|
Liao C, Rolling T, Djukovic A, Fei T, Mishra V, Liu H, Lindberg C, Dai L, Zhai B, Peled JU, van den Brink MRM, Hohl TM, Xavier JB. Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes. Nat Microbiol 2024; 9:1555-1565. [PMID: 38698178 PMCID: PMC11152985 DOI: 10.1038/s41564-024-01680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/20/2024] [Indexed: 05/05/2024]
Abstract
The detection of oral bacteria in faecal samples has been associated with inflammation and intestinal diseases. The increased relative abundance of oral bacteria in faeces has two competing explanations: either oral bacteria invade the gut ecosystem and expand (the 'expansion' hypothesis), or oral bacteria transit through the gut and their relative increase marks the depletion of other gut bacteria (the 'marker' hypothesis). Here we collected oral and faecal samples from mouse models of gut dysbiosis (antibiotic treatment and DSS-induced colitis) and used 16S ribosomal RNA sequencing to determine the abundance dynamics of oral bacteria. We found that the relative, but not absolute, abundance of oral bacteria increases, reflecting the 'marker' hypothesis. Faecal microbiome datasets from diverse patient cohorts, including healthy individuals and patients with allogeneic haematopoietic cell transplantation or inflammatory bowel disease, consistently support the 'marker' hypothesis and explain associations between oral bacterial abundance and patient outcomes consistent with depleted gut microbiota. By distinguishing between the two hypotheses, our study guides the interpretation of microbiome compositional data and could potentially identify cases where therapies are needed to rebuild the resident microbiome rather than protect against invading oral bacteria.
Collapse
Affiliation(s)
- Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thierry Rolling
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Division of Infectious Diseases, First Department of Medicine, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Ana Djukovic
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vishwas Mishra
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Medical College, New York, NY, USA
| | - Hongbin Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chloe Lindberg
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bing Zhai
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jonathan U Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
3
|
Xu Q, Zhang H, Vandenkoornhuyse P, Guo S, Kuzyakov Y, Shen Q, Ling N. Carbon starvation raises capacities in bacterial antibiotic resistance and viral auxiliary carbon metabolism in soils. Proc Natl Acad Sci U S A 2024; 121:e2318160121. [PMID: 38598339 PMCID: PMC11032446 DOI: 10.1073/pnas.2318160121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/12/2024] [Indexed: 04/12/2024] Open
Abstract
Organic carbon availability in soil is crucial for shaping microbial communities, yet, uncertainties persist concerning microbial adaptations to carbon levels and the ensuing ecological and evolutionary consequences. We investigated organic carbon metabolism, antibiotic resistance, and virus-host interactions in soils subjected to 40 y of chemical and organic fertilization that led to contrasting carbon availability: carbon-poor and carbon-rich soils, respectively. Carbon-poor soils drove the enrichment of putative genes involved in organic matter decomposition and exhibited specialization in utilizing complex organic compounds, reflecting scramble competition. This specialization confers a competitive advantage of microbial communities in carbon-poor soils but reduces their buffering capacity in terms of organic carbon metabolisms, making them more vulnerable to environmental fluctuations. Additionally, in carbon-poor soils, viral auxiliary metabolic genes linked to organic carbon metabolism increased host competitiveness and environmental adaptability through a strategy akin to "piggyback the winner." Furthermore, putative antibiotic resistance genes, particularly in low-abundance drug categories, were enriched in carbon-poor soils as an evolutionary consequence of chemical warfare (i.e., interference competition). This raises concerns about the potential dissemination of antibiotic resistance from conventional agriculture that relies on chemical-only fertilization. Consequently, carbon starvation resulting from long-term chemical-only fertilization increases microbial adaptations to competition, underscoring the importance of implementing sustainable agricultural practices to mitigate the emergence and spread of antimicrobial resistance and to increase soil carbon storage.
Collapse
Affiliation(s)
- Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
- CNRS, UMR 6553 EcoBio, Université de Rennes, Rennes Cedex35042, France
| | - He Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou730020, China
| | | | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen37077, Germany
- Department of Agricultural Soil Science, University of Göttingen, Göttingen37077, Germany
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing210095, China
| | - Ning Ling
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou730020, China
| |
Collapse
|
4
|
Tan L, Zhang D, Li YX, Li Y, Guo T, Sun Y, Li N, Feng C. Identification of intratumor bacteria-associated prognostic risk score in adrenocortical carcinoma. Microbiol Spectr 2024; 12:e0372723. [PMID: 38421176 PMCID: PMC10986527 DOI: 10.1128/spectrum.03727-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
A landmark study by Poore et al. showed intratumor bacteria (ITBs) playing a critical role in most cancers by reproduction of The Cancer Genome Atlas (TCGA) transcriptome data. A recent study by Salzberg et al. argued that ITBs, being overstated as a methodology by Poore et al., were problematic. We previously reported that ITBs were prognostic in adrenocortical carcinoma (ACC), a highly aggressive rare disease using data by Poore et al., and here, we aimed to answer whether ITBs truly existed and were prognostic in ACC. ACC samples from our institutes underwent 16S rRNA sequencing [adrenocortical carcinoma blocks from Huashan Hospital and China Medical University (HS) cohort]. The ITB profile was compared to TCGA data processed by Poore et al. (TCGA-P) and TCGA data processed by Salzberg et al. (TCGA-S), respectively. The primary outcome was overall survival (OS). A total of 26 ACC cases (HS cohort) and 10 paraffin controls were sequenced. The TCGA cohort encompassed 77 cases. Two and four amid the top 10 abundant genera in HS cohort were not detected in TCGA-P and TCGA-S, respectively. Neither was alpha or beta diversity associated with survival nor could ACC be subtyped by ITB signature in the HS cohort. Notably, a five-genera ITB risk score (Corynebacterium, Mycoplasma, Achromobacter, Anaerococcus, and Streptococcus) for OS trained in the HS cohort was validated in both TCGA-P and TCGA-S cohorts and was independently prognostic. Whereas ITB signature on the whole may not be associated with ACC subtypes, certain ITB features are associated with prognosis, and a risk score could be generated and validated externally. IMPORTANCE In this report, we looked at the role of ITBs in ACC in patients with different race and sequencing platforms. We found a five-genera ITB risk score consistently predicted overall survival in all cohorts. We conclude that certain ITB features are universally pathogenic to ACC.
Collapse
Affiliation(s)
- Linyi Tan
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Dengwei Zhang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China
| | - Yong-xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, China
| | - Yuqing Li
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ting Guo
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yang Sun
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ning Li
- Department of Urology, Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chenchen Feng
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
5
|
Roy G, Prifti E, Belda E, Zucker JD. Deep learning methods in metagenomics: a review. Microb Genom 2024; 10. [PMID: 38630611 DOI: 10.1099/mgen.0.001231] [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] [Indexed: 04/19/2024] Open
Abstract
The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome's key role in our health.
Collapse
Affiliation(s)
- Gaspar Roy
- IRD, Sorbonne University, UMMISCO, 32 avenue Henry Varagnat, Bondy Cedex, France
| | - Edi Prifti
- IRD, Sorbonne University, UMMISCO, 32 avenue Henry Varagnat, Bondy Cedex, France
- Sorbonne University, INSERM, Nutriomics, 91 bvd de l'hopital, 75013 Paris, France
| | - Eugeni Belda
- IRD, Sorbonne University, UMMISCO, 32 avenue Henry Varagnat, Bondy Cedex, France
- Sorbonne University, INSERM, Nutriomics, 91 bvd de l'hopital, 75013 Paris, France
| | - Jean-Daniel Zucker
- IRD, Sorbonne University, UMMISCO, 32 avenue Henry Varagnat, Bondy Cedex, France
- Sorbonne University, INSERM, Nutriomics, 91 bvd de l'hopital, 75013 Paris, France
| |
Collapse
|
6
|
Sansom SE, Shimasaki T, Dangana T, Lin MY, Schoeny ME, Fukuda C, Moore NM, Yelin RD, Bassis CM, Rhee Y, Cornejo Cisneros E, Bell P, Lolans K, Aboushaala K, Young VB, Hayden MK. Comparison of Daily versus Admission and Discharge Surveillance Cultures for Multidrug-Resistant Organism Detection in an Intensive Care Unit. J Infect Dis 2024:jiae162. [PMID: 38546721 DOI: 10.1093/infdis/jiae162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Admission and discharge screening of patients for asymptomatic gut colonization with multidrug-resistant organisms (MDROs) is a traditional approach to active surveillance, but its sensitivity for detecting colonization is uncertain. METHODS Daily rectal or fecal swab samples and clinical data were collected over 12 months from patients in one 25-bed intensive care unit (ICU) in Chicago, IL USA and tested for the following multidrug-resistant organisms (MDROs): vancomycin-resistant enterococci (VRE); third-generation cephalosporin-resistant Enterobacterales, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL); and carbapenem-resistant Enterobacterales (CRE). MDRO detection by (1) admission/discharge surveillance cultures or (2) clinical cultures were compared to daily surveillance cultures. Samples underwent 16S rRNA gene sequencing to measure the relative abundance of operational taxonomic units (OTUs) corresponding to each MDRO. RESULTS Compared with daily surveillance cultures, admission/discharge cultures detected 91% of prevalent MDRO colonization and 63% of incident MDRO colonization among medical ICU patients. Only a minority (7%) of MDRO carriers were identified by clinical cultures. Higher relative abundance of MDRO-associated OTUs and specific antibiotic exposures were independently associated with higher probability of MDRO detection by culture. CONCLUSION Admission and discharge surveillance cultures underestimated MDRO acquisitions in an ICU. These limitations should be considered when designing sampling strategies for epidemiologic studies that use culture-based surveillance.
Collapse
Affiliation(s)
- Sarah E Sansom
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Teppei Shimasaki
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Thelma Dangana
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Michael Y Lin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | | | - Christine Fukuda
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Nicholas M Moore
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Rachel D Yelin
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Christine M Bassis
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
| | - Yoona Rhee
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Enrique Cornejo Cisneros
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Pamela Bell
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Karen Lolans
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Khaled Aboushaala
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, MI USA
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI USA
| | - Mary K Hayden
- Department of Internal Medicine/Division of Infectious Diseases, Rush University Medical Center, Chicago, IL USA
| |
Collapse
|
7
|
Maghini DG, Oduaran OH, Wirbel J, Olubayo LAI, Smyth N, Mathema T, Belger CW, Agongo G, Boua PR, Choma SSR, Gómez-Olivé FX, Kisiangani I, Mashaba GR, Micklesfield L, Mohamed SF, Nonterah EA, Norris S, Sorgho H, Tollman S, Wafawanaka F, Tluway F, Ramsay M, Bhatt AS, Hazelhurst S. Expanding the human gut microbiome atlas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584859. [PMID: 38559015 PMCID: PMC10980044 DOI: 10.1101/2024.03.13.584859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.
Collapse
Affiliation(s)
- Dylan G Maghini
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Jakob Wirbel
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA
| | - Luicer A Ingasia Olubayo
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie Smyth
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Theophilous Mathema
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Carl W Belger
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Solomon SR Choma
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Given R Mashaba
- DIMAMO Population Health Research Centre, University of Limpopo, South Africa
| | - Lisa Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Shane Norris
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Burkina Faso
| | - Stephen Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Furahini Tluway
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Ami S Bhatt
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
8
|
Gunjur A, Shao Y, Rozday T, Klein O, Mu A, Haak BW, Markman B, Kee D, Carlino MS, Underhill C, Frentzas S, Michael M, Gao B, Palmer J, Cebon J, Behren A, Adams DJ, Lawley TD. A gut microbial signature for combination immune checkpoint blockade across cancer types. Nat Med 2024; 30:797-809. [PMID: 38429524 PMCID: PMC10957475 DOI: 10.1038/s41591-024-02823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 01/12/2024] [Indexed: 03/03/2024]
Abstract
Immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte protein 4 (CTLA-4) can induce remarkable, yet unpredictable, responses across a variety of cancers. Studies suggest that there is a relationship between a cancer patient's gut microbiota composition and clinical response to ICB; however, defining microbiome-based biomarkers that generalize across cohorts has been challenging. This may relate to previous efforts quantifying microbiota to species (or higher taxonomic rank) abundances, whereas microbial functions are often strain specific. Here, we performed deep shotgun metagenomic sequencing of baseline fecal samples from a unique, richly annotated phase 2 trial cohort of patients with diverse rare cancers treated with combination ICB (n = 106 discovery cohort). We demonstrate that strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival relative to models built using species-rank quantifications or comprehensive pretreatment clinical factors. Through a meta-analysis of gut metagenomes from a further six comparable studies (n = 364 validation cohort), we found cross-cancer (and cross-country) validity of strain-response signatures, but only when the training and test cohorts used concordant ICB regimens (anti-PD-1 monotherapy or combination anti-PD-1 plus anti-CTLA-4). This suggests that future development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen rather than according to cancer type.
Collapse
Affiliation(s)
- Ashray Gunjur
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK.
| | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Timothy Rozday
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bastiaan W Haak
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, Netherlands
| | - Ben Markman
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Alfred Health, Melbourne, Victoria, Australia
- School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Damien Kee
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Rare Cancer Laboratory, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Matteo S Carlino
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
- Melanoma Institute of Australia, University of Sydney, Sydney, New South Wales, Australia
| | - Craig Underhill
- Border Medical Oncology and Haematology Research Unit, Albury-Wodonga Regional Cancer Centre, Albury-Wodonga, New South Wales, Australia
- Rural Medical School, University of New South Wales, Albury, New South Wales, Australia
| | - Sophia Frentzas
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
| | - Michael Michael
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Bo Gao
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
| | - Jodie Palmer
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| |
Collapse
|
9
|
Ouyang C, Qin Y, Fang P, Liang Y. Methane flux at the water-gas interface is influenced by complex interactions among phytoplankton, phosphorus inputs and methane-functional bacteria: A microcosm systems study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169373. [PMID: 38104802 DOI: 10.1016/j.scitotenv.2023.169373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023]
Abstract
Phytoplankton affect carbon cycling and emissions in eutrophic reservoirs dramatically, but our knowledge about carbon emissions response to phytoplankton bloom and phosphorus enrichment is rather limited. Here we performed a microcosm experiment with five treatments to investigate how phytoplankton blooms and phosphorus addition will impact the carbon emissions and the methane-functional bacterial community. During the 43-day incubation, the CH4 and CO2 flux at the water-air interface in the five water columns fluctuated between 7.536 and 16.689 μmol and between 2788.501 and 4142.726 μmol, respectively. The flux of CH4 and CO2 during phytoplankton decay was 1.542 to 10.397 times and 4.203 to 8.622 times higher, respectively, compared to that during phytoplankton growth. Furthermore, exogenous phosphorus increases bloom biomass of phytoplankton and subsequent CH4 production, even with low nitrogen concentrations. The addition of 1 mg KH2PO4 resulted in a conservative increase of 0.0715 μmol in CH4 emission and 11.911 μmol in CO2 emission in the water column, respectively, compared to the in-situ water column. High throughput sequencing determined that hydrogenotrophic Methanoregula dominated methanogens (MPB) and Methylocystaceae dominated methanotrophs (MOB) in the sediment. Phosphorus inhibited the relative abundance of Methanoregula after incubation, resulting in a significant decrease. Real-time quantitative polymerase chain reaction indicated that the absolute abundance of MPB and MOB (i.e., the mcrA gene and the pmoA gene) in the sediments ranged from 5.1354E+06 to 6.3176E+07 copies·g-1 and 1.1656E+06 to 9.5056E+06 copies·g-1, respectively. The mcrA gene showed a preference for sediments with high organic carbon content. The effect of eutrophication on CH4 emissions is closely related to nutrient load and distinct niche of methane-functional bacteria.
Collapse
Affiliation(s)
- Changyue Ouyang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, 400074 Chongqing, China
| | - Yu Qin
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China; Key Laboratory of Hydraulic and Waterway Engineering of the Ministry of Education, Chongqing Jiaotong University, 400074 Chongqing, China.
| | - Peng Fang
- Chongqing Aerospace Rocket Electronic Technology Co., Ltd, Chongqing 400039, China
| | - Yue Liang
- School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074, China
| |
Collapse
|
10
|
Austin GI, Kav AB, Park H, Biermann J, Uhlemann AC, Korem T. Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579716. [PMID: 38405914 PMCID: PMC10888995 DOI: 10.1101/2024.02.09.579716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Every step in common microbiome profiling protocols has variable efficiency for each microbe. For example, different DNA extraction kits may have different efficiency for Gram-positive and -negative bacteria. These variable efficiencies, combined with technical variation, create strong processing biases, which impede the identification of signals that are reproducible across studies and the development of generalizable and biologically interpretable prediction models. "Batch-correction" methods have been used to alleviate these issues computationally with some success. However, many make strong parametric assumptions which do not necessarily apply to microbiome data or processing biases, or require the use of an outcome variable, which risks overfitting. Lastly and importantly, existing transformations used to correct microbiome data are largely non-interpretable, and could, for example, introduce values to features that were initially mostly zeros. Altogether, processing bias currently compromises our ability to glean robust and generalizable biological insights from microbiome data. Here, we present DEBIAS-M (Domain adaptation with phenotype Estimation and Batch Integration Across Studies of the Microbiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using benchmarks of HIV and colorectal cancer classification from gut microbiome data, and cervical neoplasia prediction from cervical microbiome data, we demonstrate that DEBIAS-M outperforms batch-correction methods commonly used in the field. Notably, we show that the inferred bias-correction factors are stable, interpretable, and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M allows for better modeling of microbiome data and identification of interpretable signals that are reproducible across studies.
Collapse
Affiliation(s)
- George I. Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aya Brown Kav
- 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
| | - Jana Biermann
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, 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
| |
Collapse
|
11
|
Zeng J, Li Y, Zou Y, Yang Y, Yang T, Zhou Y. Intestinal toxicity alleviation and efficacy potentiation through therapeutic administration of Lactobacillus paracasei GY-1 in the treatment of gout flares with colchicine. Food Funct 2024; 15:1671-1688. [PMID: 38251779 DOI: 10.1039/d3fo04858f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Gout flares have emerged as a significant public health concern. Colchicine (COL) is a first-line and standard drug for treating gout flares. However, its clinical use is limited due to various adverse effects. Besides, COL fails to adequately meet the needs of patients, particularly young patients. In this study, we investigate the therapeutic administration of Lactobacillus paracasei GY-1 (GY-1) to overcome the limitations of COL. Our results demonstrate that GY-1 attenuates COL toxicity in terms of body weight loss, decreased feed intake, mortality, reduced locomotor activity, colon shortening, increased oxidative stress, histological damage, and impaired gut permeability. Meanwhile, we demonstrate that GY-1 enhances the therapeutic effect for gout flares when combined with COL, as evidenced by the reduction in paw swelling, decreased levels of proinflammatory cytokines including IL-1β and TNF-α, and an increase in the anti-inflammatory cytokine IL-10. Additionally, the absolute quantification of the gut microbiota shows that GY-1 restores the gut microbiota imbalance caused by COL. Furthermore, GY-1 reduces the abundance of 4 Alistipes species and 6 Porphyromonadaceae species, which may be responsible for toxicity alleviation. At the same time, GY-1 increases the abundance of Bacteroides sartorii and Enterococcus sp., which may contribute to its therapeutic efficacy. This study demonstrates the feasibility of developing probiotic-based adjuvant therapy or bacteriotherapy for treating gout flares. To our knowledge, GY-1 is the first probiotic that could be used as an alternative synergetic agent with COL for the therapeutic treatment of gout flares.
Collapse
Affiliation(s)
- Jiaqi Zeng
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, Guangxi 541199, China.
| | - Yan Li
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, Guangxi 541199, China.
| | - Yizhi Zou
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, Guangxi 541199, China.
| | - Ying Yang
- Department of Public Health, School of Medicine, Guangxi University of Science and Technology, Liuzhou, Guangxi 545005, China
| | - Tingting Yang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, Guangxi 541199, China.
| | - Yizhuang Zhou
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, School of Public Health, Guilin Medical University, Guilin, Guangxi 541199, China.
| |
Collapse
|
12
|
Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
Collapse
Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
| |
Collapse
|
13
|
Zheludev IN, Edgar RC, Lopez-Galiano MJ, de la Peña M, Babaian A, Bhatt AS, Fire AZ. Viroid-like colonists of human microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576352. [PMID: 38293115 PMCID: PMC10827157 DOI: 10.1101/2024.01.20.576352] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA ~1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the "Oblins". We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in ~7% of analysed stool metatranscriptomes (29/440) and in ~50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over >300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.
Collapse
Affiliation(s)
- Ivan N Zheludev
- Stanford University, Department of Biochemistry, Stanford, CA, USA
| | | | - Maria Jose Lopez-Galiano
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain
| | - Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Valencia, Spain
| | - Artem Babaian
- University of Toronto, Department of Molecular Genetics, Ontario, Canada
- University of Toronto, Donnelly Centre for Cellular and Biomolecular Research, Ontario, Canada
| | - Ami S Bhatt
- Stanford University, Department of Genetics, Stanford, CA, USA
- Stanford University, Department of Medicine, Division of Hematology, Stanford, CA, USA
| | - Andrew Z Fire
- Stanford University, Department of Genetics, Stanford, CA, USA
- Stanford University, Department of Pathology, Stanford, CA, USA
| |
Collapse
|
14
|
Mah JC, Lohmueller KE, Garud N. Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566454. [PMID: 38014007 PMCID: PMC10680615 DOI: 10.1101/2023.11.09.566454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories and their distributions of fitness effects (DFE) of new mutations. Here, we infer the demographic histories and DFEs of 27 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find overall reductions in genetic variation among commensal gut microbes sampled from a Western population relative to an African rural population. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Taken together, these findings suggest that human commensal gut microbes have distinct evolutionary histories, possibly reflecting the unique roles of individual members of the microbiome.
Collapse
|
15
|
Littlejohn PT, Glover JS. Ethical gut microbiota research in Africa. Nat Microbiol 2023; 8:1376-1377. [PMID: 37460625 DOI: 10.1038/s41564-023-01436-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Affiliation(s)
- Paula T Littlejohn
- Department of Medical Genetics, Center for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia School of Medicine, Vancouver, British Columbia, Canada.
- Department of Pediatrics, Division of Gastroenterology, BC Children's Hospital Research Institute, University of British Columbia School of Medicine, Vancouver, British Columbia, Canada.
| | - Janiece S Glover
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.
| |
Collapse
|