1
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [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: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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2
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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3
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Dai C, Chen X, Qian S, Fan Y, Li L, Yuan J. Dysbiosis of intestinal homeostasis contribute to Whitmania pigra edema disease. Microb Biotechnol 2023; 16:1940-1956. [PMID: 37410351 PMCID: PMC10527190 DOI: 10.1111/1751-7915.14308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023] Open
Abstract
Whitmania pigra is widely used in traditional Chinese medicine. However, W. pigra is being threatened by an edema disease with unknown causes (WPE). In this study, a comprehensive exploration of virome, microbiome, and metabolome aberrations in the intestine of W. pigra was performed to address the aetiology of WPE. Virome analysis indicated that eukaryotic viruses did not contribute to WPE, whereas an expansion of Caudovirales was observed in WPE. Compared to the control, the microbial richness and diversity in diseased W. pigra decreased remarkably. Nine genera, including Aeromonas, Anaerotruncus, Vibrio, Proteocatella, Acinetobacter, and Brachyspira were overrepresented in WPE, whereas eleven genera, including Bifidobacterium, Phascolarctobacterium, Lactobacillus, Bacillus and AF12, were enriched in healthy individuals. Furthermore, certain metabolites, especially amino acids, short-chain fatty acids, and bile acids, were found to be linked to intestinal microbiota alterations in WPE. An integration of the microbiome and metabolome in WPE found that dysbiosis of the gut microbiota or metabolites caused WPE. Notably, W. pigra accepted intestinal microbiota transplantation from WPE donors developed WPE clinical signs eventually, and the dysbiotic intestinal microbiota can be recharacterized in this recipient W. pigra. Strikingly, pathological features of metanephridium and uraemic toxin enrichment in the gut indicated a putative interconnection between the gut and metanephridium in WPE, which represents the prototype of the gut-kidney axis in mammals. These finding exemplify the conservation of "microecological Koch's postulates" from annelids to insects and other vertebrates, which provides a direction of prevention and treatment for WPE and opens a new insight into the pathogenesis of aquatic animal diseases from an ecological perspective.
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Affiliation(s)
- Caijiao Dai
- Department of Aquatic Animal Medicine, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- National Aquatic Animal Diseases Para‐reference laboratory (HZAU)WuhanChina
| | - Xin Chen
- Department of Aquatic Animal Medicine, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- National Aquatic Animal Diseases Para‐reference laboratory (HZAU)WuhanChina
| | - Shiyu Qian
- Department of Aquatic Animal Medicine, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- Hubei Engineering Research Centre for Aquatic Animal Diseases Control and PreventionWuhanChina
| | - Yihui Fan
- Department of Aquatic Animal Medicine, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- Hubei Engineering Research Centre for Aquatic Animal Diseases Control and PreventionWuhanChina
| | - Lijuan Li
- Department of Aquatic Animal Medicine, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- National Aquatic Animal Diseases Para‐reference laboratory (HZAU)WuhanChina
- Hubei Engineering Research Centre for Aquatic Animal Diseases Control and PreventionWuhanChina
| | - Junfa Yuan
- Department of Aquatic Animal Medicine, College of FisheriesHuazhong Agricultural UniversityWuhanChina
- National Aquatic Animal Diseases Para‐reference laboratory (HZAU)WuhanChina
- Hubei Engineering Research Centre for Aquatic Animal Diseases Control and PreventionWuhanChina
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4
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Hornburg D, Wu S, Moqri M, Zhou X, Contrepois K, Bararpour N, Traber GM, Su B, Metwally AA, Avina M, Zhou W, Ubellacker JM, Mishra T, Schüssler-Fiorenza Rose SM, Kavathas PB, Williams KJ, Snyder MP. Dynamic lipidome alterations associated with human health, disease and ageing. Nat Metab 2023; 5:1578-1594. [PMID: 37697054 PMCID: PMC10513930 DOI: 10.1038/s42255-023-00880-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 07/28/2023] [Indexed: 09/13/2023]
Abstract
Lipids can be of endogenous or exogenous origin and affect diverse biological functions, including cell membrane maintenance, energy management and cellular signalling. Here, we report >800 lipid species, many of which are associated with health-to-disease transitions in diabetes, ageing and inflammation, as well as cytokine-lipidome networks. We performed comprehensive longitudinal lipidomic profiling and analysed >1,500 plasma samples from 112 participants followed for up to 9 years (average 3.2 years) to define the distinct physiological roles of complex lipid subclasses, including large and small triacylglycerols, ester- and ether-linked phosphatidylethanolamines, lysophosphatidylcholines, lysophosphatidylethanolamines, cholesterol esters and ceramides. Our findings reveal dynamic changes in the plasma lipidome during respiratory viral infection, insulin resistance and ageing, suggesting that lipids may have roles in immune homoeostasis and inflammation regulation. Individuals with insulin resistance exhibit disturbed immune homoeostasis, altered associations between lipids and clinical markers, and accelerated changes in specific lipid subclasses during ageing. Our dataset based on longitudinal deep lipidome profiling offers insights into personalized ageing, metabolic health and inflammation, potentially guiding future monitoring and intervention strategies.
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Affiliation(s)
- Daniel Hornburg
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Si Wu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mahdi Moqri
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Xin Zhou
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Nasim Bararpour
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gavin M Traber
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Baolong Su
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Monica Avina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Jessalyn M Ubellacker
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Paula B Kavathas
- Departments of Laboratory Medicine and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Kevin J Williams
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Lipidomics Laboratory, University of California, Los Angeles, Los Angeles, CA, USA
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5
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Hajjar R, Gonzalez E, Fragoso G, Oliero M, Alaoui AA, Calvé A, Vennin Rendos H, Djediai S, Cuisiniere T, Laplante P, Gerkins C, Ajayi AS, Diop K, Taleb N, Thérien S, Schampaert F, Alratrout H, Dagbert F, Loungnarath R, Sebajang H, Schwenter F, Wassef R, Ratelle R, Debroux E, Cailhier JF, Routy B, Annabi B, Brereton NJB, Richard C, Santos MM. Gut microbiota influence anastomotic healing in colorectal cancer surgery through modulation of mucosal proinflammatory cytokines. Gut 2022; 72:1143-1154. [PMID: 36585238 DOI: 10.1136/gutjnl-2022-328389] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Colorectal cancer (CRC) is the third most diagnosed cancer, and requires surgical resection and reconnection, or anastomosis, of the remaining bowel to re-establish intestinal continuity. Anastomotic leak (AL) is a major complication that increases mortality and cancer recurrence. Our objective is to assess the causal role of gut microbiota in anastomotic healing. DESIGN The causal role of gut microbiota was assessed in a murine AL model receiving faecal microbiota transplantation (FMT) from patients with CRC collected before surgery and who later developed or not, AL. Anastomotic healing and gut barrier integrity were assessed after surgery. Bacterial candidates implicated in anastomotic healing were identified using 16S rRNA gene sequencing and were isolated from faecal samples to be tested both in vitro and in vivo. RESULTS Mice receiving FMT from patients that developed AL displayed poor anastomotic healing. Profiling of gut microbiota of patients and mice after FMT revealed correlations between healing parameters and the relative abundance of Alistipes onderdonkii and Parabacteroides goldsteinii. Oral supplementation with A. onderdonkii resulted in a higher rate of leaks in mice, while gavage with P. goldsteinii improved healing by exerting an anti-inflammatory effect. Patients with AL and mice receiving FMT from AL patients presented upregulation of mucosal MIP-1α, MIP-2, MCP-1 and IL-17A/F before surgery. Retrospective analysis revealed that patients with AL present higher circulating neutrophil and monocyte counts before surgery. CONCLUSION Gut microbiota plays an important role in surgical colonic healing in patients with CRC. The impact of these findings may extend to a vast array of invasive gastrointestinal procedures.
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Affiliation(s)
- Roy Hajjar
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Department of Surgery, Université de Montréal, Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Gabriela Fragoso
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Manon Oliero
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Ahmed Amine Alaoui
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Department of Surgery, Université de Montréal, Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Annie Calvé
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Hervé Vennin Rendos
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Souad Djediai
- Molecular Oncology Laboratory, Department of Chemistry, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
| | - Thibault Cuisiniere
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Patrick Laplante
- Institut du cancer de Montréal, Montréal, Québec, Canada.,Axe Cancer, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Claire Gerkins
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Ayodeji Samuel Ajayi
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Khoudia Diop
- Institut du cancer de Montréal, Montréal, Québec, Canada.,Laboratory of Immunotherapy and Oncomicrobiome, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Nassima Taleb
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Sophie Thérien
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Frédéricke Schampaert
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Hefzi Alratrout
- (Current address: Department of General Surgery, King Fahd Hospital of the University, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia). Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - François Dagbert
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Rasmy Loungnarath
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Herawaty Sebajang
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Frank Schwenter
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Ramses Wassef
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Richard Ratelle
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Eric Debroux
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Jean-François Cailhier
- Institut du cancer de Montréal, Montréal, Québec, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada.,Renal Division, Department of Medicine, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Bertrand Routy
- Institut du cancer de Montréal, Montréal, Québec, Canada.,Laboratory of Immunotherapy and Oncomicrobiome, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Hemato-oncology Division, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada
| | - Borhane Annabi
- Molecular Oncology Laboratory, Department of Chemistry, Université du Québec à Montréal (UQAM), Montréal, Québec, Canada
| | - Nicholas J B Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.,Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Carole Richard
- Digestive Surgery Service, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec, Canada.,Division of General Surgery, Université de Montréal, Montréal, Québec, Canada
| | - Manuela M Santos
- Nutrition and Microbiome Laboratory, Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada .,Institut du cancer de Montréal, Montréal, Québec, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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6
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Zhou X, Wang B, Demkowicz PC, Johnson JS, Chen Y, Spakowicz DJ, Zhou Y, Dorsett Y, Chen L, Sodergren E, Kuchel GA, Weinstock GM. Exploratory studies of oral and fecal microbiome in healthy human aging. FRONTIERS IN AGING 2022; 3:1002405. [PMID: 36338834 PMCID: PMC9631447 DOI: 10.3389/fragi.2022.1002405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
Abstract
Growing evidence has linked an altered host fecal microbiome composition with health status, common chronic diseases, and institutionalization in vulnerable older adults. However, fewer studies have described microbiome changes in healthy older adults without major confounding diseases or conditions, and the impact of aging on the microbiome across different body sites remains unknown. Using 16S ribosomal RNA gene sequencing, we reconstructed the composition of oral and fecal microbiomes in young (23-32; mean = 25 years old) and older (69-94; mean = 77 years old) healthy community-dwelling research subjects. In both body sites, we identified changes in minor bacterial operational taxonomic units (OTUs) between young and older subjects. However, the composition of the predominant bacterial species of the healthy older group in both microbiomes was not significantly different from that of the young cohort, which suggests that dominant bacterial species are relatively stable with healthy aging. In addition, the relative abundance of potentially pathogenic genera, such as Rothia and Mycoplasma, was enriched in the oral microbiome of the healthy older group relative to the young cohort. We also identified several OTUs with a prevalence above 40% and some were more common in young and others in healthy older adults. Differences with aging varied for oral and fecal samples, which suggests that members of the microbiome may be differentially affected by aging in a tissue-specific fashion. This is the first study to investigate both oral and fecal microbiomes in the context of human aging, and provides new insights into interactions between aging and the microbiome within two different clinically relevant sites.
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Affiliation(s)
- Xin Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - Baohong Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, Hangzhou City, China
| | - Patrick C. Demkowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Yale University School of Medicine, New Haven, CT, United States
| | - Jethro S. Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Yanfei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University School of Medicine, Hangzhou City, China
| | - Daniel J. Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, United States
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - George A. Kuchel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- UConn Center on Aging, University of Connecticut Health Center, Farmington, CT, United States
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Yang K, Deng X, Jian S, Zhang M, Wen C, Xin Z, Zhang L, Tong A, Ye S, Liao P, Xiao Z, He S, Zhang F, Deng J, Zhang L, Deng B. Gallic Acid Alleviates Gut Dysfunction and Boosts Immune and Antioxidant Activities in Puppies Under Environmental Stress Based on Microbiome-Metabolomics Analysis. Front Immunol 2022; 12:813890. [PMID: 35095912 PMCID: PMC8795593 DOI: 10.3389/fimmu.2021.813890] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
Early-life exposure to environmental stress disrupts the gut barrier and leads to inflammatory responses and changes in gut microbiota composition. Gallic acid (GA), a natural plant polyphenol, has received significant interest for its antioxidant, anti-inflammatory, and antimicrobial properties that support the maintenance of intestinal health. To assess whether dietary supplementation of GA alleviates environmental stress, a total of 19 puppies were randomly allocated to the following three dietary treatments for 2 weeks: 1) basal diet (control (CON)); 2) basal diet + transportation (TS); and 3) basal diet with the addition of 500 mg/kg of GA + transportation (TS+GA). After a 1-week supplementation period, puppies in the TS and TS+GA groups were transported from a stressful environment to another livable location, and puppies in the CON group were then left in the stressful environment. Results indicated that GA markedly reduced the diarrhea rate in puppies throughout the trial period and caused a moderate decline of serum cortisol and HSP-70 levels after transportation. Also, GA alleviated the oxidative stress and inflammatory response caused by multiple environmental stressors. Meanwhile, puppies fed GA had a higher abundance of fecal Firmicutes and Lactobacillus and lower Proteobacteria, Escherichia–Shigella, and Clostridium_sensu_stricto_1 after transportation. As a result, the TS+GA group had the highest total short-chain fatty acids and acetic acid. Also, the fecal and serum metabolomics analyses revealed that GA markedly reversed the abnormalities of amino acid metabolism, lipid metabolism, carbohydrate metabolism, and nucleotide metabolism caused by stresses. Finally, Spearman’s correlation analysis was carried out to explore the comprehensive microbiota and metabolite relationships. Overall, dietary supplementation of GA alleviates oxidative stress and inflammatory response in stressed puppies by causing beneficial shifts on gut microbiota and metabolites that may support gut and host health.
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Affiliation(s)
- Kang Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiaolin Deng
- Department of Urology, Ganzhou People's Hospital, Ganzhou, China
| | - Shiyan Jian
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Meiyu Zhang
- College of Animal Science and Technology, Guangdong Polytechnic of Science and Trade, Guangzhou, China
| | - Chaoyu Wen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zhongquan Xin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Limeng Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Aorigeile Tong
- Research Center of Pet Nutrition, Guangzhou Qingke Biotechnology Co., Ltd., Guangzhou, China
| | - Shibin Ye
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Pinfeng Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Zaili Xiao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shansong He
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Fan Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jinping Deng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lingna Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Baichuan Deng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, China
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