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Xue H, Wang Y, Mei C, Han L, Lu M, Li X, Chen T, Wang F, Tang X. Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP). mSystems 2024:e0083924. [PMID: 39320101 DOI: 10.1128/msystems.00839-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 09/26/2024] Open
Abstract
Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption. Recent evidence suggests that the gut microbiome may influence lactose levels in the gut. However, there is limited understanding regarding the alterations in microbiota and metabolism between individuals with LI and non-LI. This study conducted a paired-sample investigation utilizing data from the American Gut Project (AGP) and performed metagenomic and untargeted metabolomic analyses in a Chinese cohort to explore the interaction between the gut microbiome and serum metabolites. In addition, fecal microbiota transplantation (FMT) experiments were conducted to further examine the impact of the LI-associated gut microbiome on inflammatory outcomes. We identified 14 microbial genera that significantly differed between LI and controls from AGP data. Using a machine learning approach, group separation was predicted based on seven species and nine metabolites in the Chinese cohort. Notably, increased levels of Escherichia coli in the LI group were negatively correlated with several metabolites, including PC (22:6/0:0), indole, and Lyso PC, while reduced levels of Faecalibacterium prausnitzii and Eubacterium rectale were positively correlated with indole and furazolidone. FMT-LI rats displayed visceral hypersensitivity and an altered gut microbiota composition compared to FMT-HC rats. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI, which was confirmed by FMT-LI rats showing higher expression of ERK and RAS, along with increased concentrations of proinflammatory cytokines. This study provides valuable insights into the disrupted microbial and metabolic traits associated with LI, emphasizing potential microbiome-based approaches for its prevention and treatment. IMPORTANCE Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms after lactose consumption due to a deficiency of lactase. There is limited understanding regarding the microbiota and metabolic alterations between individuals with LI and non-LI. This study represents the first exploration to investigate metagenomic and metabolomic signatures among subjects with lactose intolerance as far as our knowledge. We identified 14 microbial genera in the Western cohort and 7 microbial species, along with 9 circulating metabolites in the Chinese cohort, which significantly differed in LI patients. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI patients. This finding was confirmed by FMT-LI rats, exhibiting increased expression of ERK and RAS, along with higher concentrations of pro-inflammatory cytokines. Our study provides insights into the disrupted functional and metabolic traits of the gut microbiome in LI, highlighting potential microbiome-based approaches for preventing and treating LI.
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Affiliation(s)
- Hong Xue
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yitian Wang
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chunfeng Mei
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lili Han
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengxiong Lu
- Department of Integrated Traditional Chinese and Western Medicine, Peking University Health Science Center, Beijing, China
- Department of Gastrointestinal Medicine, Peking University Traditional Chinese Medicine Clinical Medical School (Xiyuan), Beijing, China
| | - Xuan Li
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ting Chen
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengyun Wang
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xudong Tang
- Digestive Laboratory of Traditional Chinese Medicine, Research Institute of Spleen and Stomach Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Department of Integrated Traditional Chinese and Western Medicine, Peking University Health Science Center, Beijing, China
- Department of Gastrointestinal Medicine, Peking University Traditional Chinese Medicine Clinical Medical School (Xiyuan), Beijing, China
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Ma Z, Zuo T, Frey N, Rangrez AY. A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation. Signal Transduct Target Ther 2024; 9:237. [PMID: 39307902 PMCID: PMC11418828 DOI: 10.1038/s41392-024-01946-6] [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: 03/05/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 09/26/2024] Open
Abstract
The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.
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Affiliation(s)
- Ziqi Ma
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Tao Zuo
- Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Norbert Frey
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
| | - Ashraf Yusuf Rangrez
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany.
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Smibert OC, Trubiano JA, Kwong JC, Markey KA, Slavin MA. Protocol for a clinically annotated biorepository of samples from Australian immune-compromised patients to investigate the host-microbiome interaction. BMJ Open 2024; 14:e085504. [PMID: 39266311 DOI: 10.1136/bmjopen-2024-085504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/14/2024] Open
Abstract
INTRODUCTION The human gut microbiota has the potential to modulate the outcomes of several human diseases. This effect is likely to be mediated through interaction with the host immune system. This protocol details the establishment of a biorepository of clinically annotated samples, which we will use to explore correlations between the gut microbiota and the immune system of immune-compromised patients. We aim to identify microbiome-related risk factors for adverse outcomes. METHODS AND ANALYSES This is a protocol for the development of a biorepository of clinically annotated samples collected prospectively across three centres in Melbourne, Australia. Participants will be recruited across the following clinical streams: (1) acute leukaemia and allogeneic stem cell transplant; (2) end-stage liver disease and liver transplant; (3) patients receiving any cancer immunotherapies (eg, chimeric antigen receptor therapy); (4) deceased organ donors and (5) healthy adult controls. Participants will be asked to provide paired peripheral blood and microbiota samples (stool and saliva) at either (1) single time point for healthy controls and deceased organ donors or (2) longitudinally over multiple prespecified or event-driven time points for the remaining cohorts. Sampling of fluid from bronchoalveolar lavage and colonoscopy or biopsy of tissues undertaken during routine care will also be performed. ETHICS AND DISSEMINATION Ethical approval has been obtained from the relevant local ethics committee (The Royal Melbourne Hospital Human Research Ethics Committee). The results of this study will be disseminated by various scientific platforms including social media, international presentations and publication in peer-reviewed journals. TRIAL REGISTRATION NUMBER ACTRN12623001105639. Date registered 20 October 2023.
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Affiliation(s)
- Olivia C Smibert
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Infectious Diseases & Immunology, Austin Health, Melbourne, Victoria, Australia
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jason A Trubiano
- Department of Infectious Diseases & Immunology, Austin Health, Melbourne, Victoria, Australia
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Antibiotic Allergy and Research, Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Jason C Kwong
- Department of Infectious Diseases & Immunology, Austin Health, Melbourne, Victoria, Australia
- Department of Microbiology & Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kate A Markey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Monica A Slavin
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Infectious Diseases, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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Li J, Ghosh TS, Arendt E, Shanahan F, O'Toole PW. Cross-Cohort Gut Microbiome Signatures of Irritable Bowel Syndrome Presentation and Treatment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308313. [PMID: 39243395 DOI: 10.1002/advs.202308313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 07/02/2024] [Indexed: 09/09/2024]
Abstract
Irritable bowel syndrome (IBS) is a prevalent disorder of gut-brain interaction without a reliable cure. Evidence suggests that an alteration of the gut microbiome may contribute to IBS pathogenesis, motivating the development of microbiome-targeted therapies to alleviate IBS symptoms. However, IBS-specific microbiome signatures are variable across cohorts. A total of 9204 datasets were meta-analyzed, derived from fourteen IBS microbiome discovery cohorts, three validation cohorts for diet-microbiome interactions, and five rifaximin therapy cohorts. The consistent bacterial species and functional signatures associated with IBS were identified. Network analysis revealed two distinct IBS-enriched microbiota clusters; obligate anaerobes that are found commonly in the gut, and facultative anaerobes typically present in the mouth, implying a possible association between oral bacterial translocation to gut and IBS pathogenesis. By analyzing diet-microbiome interactions, microbiota-targeted diets that can potentially modulate the altered gut microbiota of IBS subjects toward a healthy status were identified. Furthermore, rifaximin treatment of IBS subjects was linked with a reduction in the abundance of facultatively anaerobic pathobionts. Gut microbiome signatures were identified across IBS cohorts that may inform the development of therapies for microbiome modulation in IBS. The microbiota-targeted diet patterns described may enable nutritional intervention trials in IBS and for assisting dietary management.
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Affiliation(s)
- Junhui Li
- APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
- School of Microbiology, University College Cork, Cork, T12 K8AF, Ireland
| | - Tarini Shankar Ghosh
- APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
- School of Microbiology, University College Cork, Cork, T12 K8AF, Ireland
| | - Elke Arendt
- APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
- School of Food and Nutritional Sciences, University College Cork, Cork, T12 K8AF, Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
- Department of Medicine, University College Cork, Cork, T12 K8AF, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, T12 K8AF, Ireland
- School of Microbiology, University College Cork, Cork, T12 K8AF, Ireland
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Jiang SS, Kang ZR, Chen YX, Fang JY. The gut microbiome modulate response to immunotherapy in cancer. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2634-7. [PMID: 39235561 DOI: 10.1007/s11427-023-2634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/05/2024] [Indexed: 09/06/2024]
Abstract
Gut microbiota have been reported to play an important role in the occurrence and development of malignant tumors. Currently, clinical studies have identified specific gut microbiota and its metabolites associated with efficacy of immunotherapy in multiple types of cancers. Preclinical investigations have elucidated that gut microbiota modulate the antitumor immunity and affect the efficacy of cancer immunotherapy. Certain microbiota and its metabolites may favorably remodel the tumor microenvironment by engaging innate and/or adaptive immune cells. Understanding how the gut microbiome interacts with cancer immunotherapy opens new avenues for improving treatment strategies. Fecal microbial transplants, probiotics, dietary interventions, and other strategies targeting the microbiota have shown promise in preclinical studies to enhance the immunotherapy. Ongoing clinical trials are evaluating these approaches. This review presents the recent advancements in understanding the dynamic interplay among the host immunity, the microbiome, and cancer immunotherapy, as well as strategies for modulating the microbiome, with a view to translating into clinical applications.
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Affiliation(s)
- Shan-Shan Jiang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Zi-Ran Kang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Ying-Xuan Chen
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200001, China.
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6
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Li J, O’Toole PW. Disease-associated microbiome signature species in the gut. PNAS NEXUS 2024; 3:pgae352. [PMID: 39228810 PMCID: PMC11370893 DOI: 10.1093/pnasnexus/pgae352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
There is an accumulation of evidence that the human gut microbiota plays a role in maintaining health, and that an altered gut microbiota (sometimes called dysbiosis) associates with risk for many noncommunicable diseases. However, the dynamics of disease-linked bacteria in the gut and other body sites remain unclear. If microbiome alterations prove causative in particular diseases, therapeutic intervention may be possible. Furthermore, microbial signature taxa have been established for the diagnosis of some diseases like colon cancer. We identified 163 disease-enriched and 98 disease-depleted gut microbiome signature taxa at species-level resolution (signature species) from 10 meta-analyses of multiple diseases such as colorectal cancer, ulcerative colitis, Crohn's disease, irritable bowel syndrome, pancreatic cancer, and COVID-19 infection. Eight signature species were enriched and nine were depleted across at least half of the diseases studied. Compared with signature species depleted in diseases, a significantly higher proportion of disease-enriched signature species were identified as extra-intestinal (primarily oral) inhabitants, had been reported in bacteremia cases from the literature, and were aerotolerant anaerobes. These findings highlight the potential involvement of oral microbes, bacteremia isolates, and aerotolerant anaerobes in disease-associated gut microbiome alterations, and they have implications for patient care and disease management.
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Affiliation(s)
- Junhui Li
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
- School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
| | - Paul W O’Toole
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
- School of Microbiology, University College Cork, Cork T12 K8AF, Ireland
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7
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Mohr AE, Jasbi P, van Woerden I, Chi J, Gu H, Bruening M, Whisner CM. Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort. GUT MICROBES REPORTS 2024; 1:1-23. [PMID: 39221110 PMCID: PMC11361303 DOI: 10.1080/29933935.2024.2387936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.
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Affiliation(s)
- Alex E. Mohr
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Center for Personalized Diagnostics, School of Molecular Sciences, Arizona State University, Tempe, AZ USA
| | - Irene van Woerden
- Community and Public Health, Idaho State University, Pocatello, ID, USA
| | - Jinhua Chi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Meg Bruening
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Department of Nutritional Sciences, College of Health and Human Development, Pennsylvania State University, University Park, PA, USA
| | - Corrie M. Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
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Zugman M, Wong M, Jaime-Casas S, Pal SK. The gut microbiome and dietary metabolites in the treatment of renal cell carcinoma. Urol Oncol 2024:S1078-1439(24)00540-4. [PMID: 39095306 DOI: 10.1016/j.urolonc.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/13/2024] [Accepted: 07/02/2024] [Indexed: 08/04/2024]
Abstract
The gut microbiome is interlinked with renal cell carcinoma (RCC) and its response to systemic treatment. Mounting data suggests that certain elements of the gut microbiome may correlate with improved outcomes. New generation sequencing techniques and advanced bioinformatic data curation are accelerating the investigation of specific markers and metabolites that could predict treatment response. A variety of new therapeutic strategies, such as fecal microbiota transplantation, probiotic supplements, and dietary interventions, are currently being developed to modify the gut microbiome and improve anticancer therapies in patients with RCC. This review discusses the preliminary evidence indicating the role of the microbiome in cancer treatment, the techniques and tools necessary for its proper study and some of the current forms with which the microbiome can be modulated to improve patient outcomes.
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Affiliation(s)
- Miguel Zugman
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA; Centro de Oncologia e Hematologia Família Dayan-Daycoval Einstein, Hospital Israelita Albert, São Paulo, São Paulo, Brazil
| | - Megan Wong
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Salvador Jaime-Casas
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Sumanta K Pal
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA.
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Meloncelli N, O'Connor H, de Jersey S, Rushton A, Pateman K, Gallaher S, Kearney L, Wilkinson S. Designing a behaviour change intervention using COM-B and the Behaviour Change Wheel: Co-designing the Healthy Gut Diet for preventing gestational diabetes. J Hum Nutr Diet 2024. [PMID: 39054768 DOI: 10.1111/jhn.13355] [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: 02/12/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Evidence suggests that modulating the gut microbiota during pregnancy may help prevent gestational diabetes mellitus (GDM). The Healthy Gut Diet study is a complex behaviour change intervention co-designed with women who have a lived experience of GDM. The aim of the study was to describe the development of the behaviour change dietary intervention, the Healthy Gut Diet. METHODS This study followed the process for designing behaviour change interventions using the Behaviour Change Wheel. Six researchers and 12 women with lived experience participated in online workshops to co-design the Healthy Gut Diet intervention. This included "diagnosing" the barriers and enablers to two target behaviours: eating more plant foods and eating less ultra processed/saturated fat containing foods. Content analysis of the workshop transcripts and activities was undertaken, underpinned by the Capability, Opportunity, Motivation and Behaviour (COM-B) model and the Theoretical Domains Framework (TDF). RESULTS Barriers and enablers to the target behaviours were described across all six COM-B components and 10 TDF domains. The intervention functions for the Healthy Gut Diet were education, enablement, environmental restructuring, persuasion and incentivisation. Forty behaviour change techniques were integrated into five modes of delivery for the Healthy Gut Diet intervention. The feasibility, acceptability and effectiveness of the Healthy Gut Diet is being tested within a randomised controlled trial. CONCLUSIONS Using the Behaviour Change Wheel process in partnership with consumers resulted in a clearly described complex intervention targeting barriers and enablers of dietary behaviour change to improve the gut microbiota diversity in pregnant women.
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Affiliation(s)
- Nina Meloncelli
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Office of the Chief Allied Health Practitioner, Metro North Health, Herston, QLD, Australia
| | - Hannah O'Connor
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Dietetics and Foodservices, Royal Brisbane and Women's Hospital, Metro North Health, Herston, QLD, Australia
| | - Susan de Jersey
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Dietetics and Foodservices, Royal Brisbane and Women's Hospital, Metro North Health, Herston, QLD, Australia
| | - Alita Rushton
- Office of the Chief Allied Health Practitioner, Metro North Health, Herston, QLD, Australia
| | - Kelsey Pateman
- Centre for Allied Health Research, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- School of Dentistry, The University of Queensland, Herston, QLD, Australia
| | | | - Lauren Kearney
- School of Nursing, Midwifery and Social Work, The University of Queensland, Brisbane, QLD, Australia
- Women's and Newborn Service Group, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Shelley Wilkinson
- Department of Obstetric Medicine, Mater Mothers Hospitals, South Brisbane, QLD, Australia
- School of Pharmacy, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD, Australia
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10
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Johnson-Martínez JP, Diener C, Levine AE, Wilmanski T, Suskind DL, Ralevski A, Hadlock J, Magis AT, Hood L, Rappaport N, Gibbons SM. Aberrant bowel movement frequencies coincide with increased microbe-derived blood metabolites associated with reduced organ function. Cell Rep Med 2024; 5:101646. [PMID: 39019013 PMCID: PMC11293344 DOI: 10.1016/j.xcrm.2024.101646] [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: 04/11/2023] [Revised: 02/22/2024] [Accepted: 06/14/2024] [Indexed: 07/19/2024]
Abstract
Bowel movement frequency (BMF) directly impacts the gut microbiota and is linked to diseases like chronic kidney disease or dementia. In particular, prior work has shown that constipation is associated with an ecosystem-wide switch from fiber fermentation and short-chain fatty acid production to more detrimental protein fermentation and toxin production. Here, we analyze multi-omic data from generally healthy adults to see how BMF affects their molecular phenotypes, in a pre-disease context. Results show differential abundances of gut microbial genera, blood metabolites, and variation in lifestyle factors across BMF categories. These differences relate to inflammation, heart health, liver function, and kidney function. Causal mediation analysis indicates that the association between lower BMF and reduced kidney function is partially mediated by the microbially derived toxin 3-indoxyl sulfate (3-IS). This result, in a generally healthy context, suggests that the accumulation of microbiota-derived toxins associated with abnormal BMF precede organ damage and may be drivers of chronic, aging-related diseases.
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Affiliation(s)
- Johannes P Johnson-Martínez
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Christian Diener
- Institute for Systems Biology, Seattle, WA 98109, USA; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Anne E Levine
- Institute for Systems Biology, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | | | | | | | - Jennifer Hadlock
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Biomedical Informatics, University of Washington, Seattle, WA 98104 USA
| | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Phenome Health, Seattle, WA 98109, USA; Department of Immunology, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Center for Phenomic Health, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Noa Rappaport
- Institute for Systems Biology, Seattle, WA 98109, USA; Phenome Health, Seattle, WA 98109, USA; Center for Phenomic Health, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; eScience Institute, University of Washington, Seattle, WA 98195, USA.
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11
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Huang Y, Xu W, Dong W, Chen G, Sun Y, Zeng X. Anti-diabetic effect of dicaffeoylquinic acids is associated with the modulation of gut microbiota and bile acid metabolism. J Adv Res 2024:S2090-1232(24)00264-9. [PMID: 38969095 DOI: 10.1016/j.jare.2024.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/06/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024] Open
Abstract
INTRODUCTION The human gut microbiome plays a pivotal role in health and disease, notably through its interaction with bile acids (BAs). BAs, synthesized in the liver, undergo transformation by the gut microbiota upon excretion into the intestine, thus influencing host metabolism. However, the potential mechanisms of dicaffeoylquinic acids (DiCQAs) from Ilex kudingcha how to modulate lipid metabolism and inflammation via gut microbiota remain unclear. OBJECTIVES AND METHODS The objectives of the present study were to investigate the regulating effects of DiCQAs on diabetes and the potential mechanisms of action. Two mice models were utilized to investigate the anti-diabetic effects of DiCQAs. Additionally, analysis of gut microbiota structure and functions was conducted concurrently with the examination of DiCQAs' impact on gut microbiota carrying the bile salt hydrolase (BSH) gene, as well as on the enterohepatic circulation of BAs and related signaling pathways. RESULTS Our findings demonstrated that DiCQAs alleviated diabetic symptoms by modulating gut microbiota carrying the BSH gene. This modulation enhanced intestinal barrier integrity, increased enterohepatic circulation of conjugated BAs, and inhibited the farnesoid X receptor-fibroblast growth factor 15 (FGF15) signaling axis in the ileum. Consequently, the protein expression of hepatic FGFR4 fibroblast growth factor receptor 4 (FGFR4) decreased, accompanied by heightened BA synthesis, reduced hepatic BA stasis, and lowered levels of hepatic and plasma cholesterol. Furthermore, DiCQAs upregulated glucolipid metabolism-related proteins in the liver and muscle, including v-akt murine thymoma viral oncogene homolog (AKT)/glycogen synthase kinase 3-beta (GSK3β) and AMP-activated protein kinase (AMPK), thereby ameliorating hyperglycemia and mitigating inflammation through the down-regulation of the MAPK signaling pathway in the diabetic group. CONCLUSION Our study elucidated the anti-diabetic effects and mechanism of DiCQAs from I. kudingcha, highlighting the potential of targeting gut microbiota, particularly Acetatifactor sp011959105 and Acetatifactor muris carrying the BSH gene, as a therapeutic strategy to attenuate FXR-FGF15 signaling and ameliorate diabetes.
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Affiliation(s)
- Yujie Huang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; School of Public Health, Guizhou Medical University, Guiyang 561113, Guizhou, China
| | - Weiqi Xu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Wei Dong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Guijie Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yi Sun
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xiaoxiong Zeng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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12
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Basuray N, Deehan EC, Vieira FT, Avedzi HM, Duke RL, Colín-Ramírez E, Tun HM, Zhang Z, Wine E, Madsen KL, Field CJ, Haqq AM. Dichotomous effect of dietary fiber in pediatrics: a narrative review of the health benefits and tolerance of fiber. Eur J Clin Nutr 2024; 78:557-568. [PMID: 38480843 DOI: 10.1038/s41430-024-01429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024]
Abstract
Dietary fibers are associated with favorable gastrointestinal, immune, and metabolic health outcomes when consumed at sufficient levels. Despite the well-described benefits of dietary fibers, children and adolescents continue to fall short of daily recommended levels. This gap in fiber intake (i.e., "fiber gap") might increase the risk of developing early-onset pediatric obesity and obesity-related comorbidities such as type 2 diabetes mellitus into adulthood. The structure-dependent physicochemical properties of dietary fiber are diverse. Differences in solubility, viscosity, water-holding capacity, binding capability, bulking effect, and fermentability influence the physiological effects of dietary fibers that aid in regulating appetite, glycemic and lipidemic responses, and inflammation. Of growing interest is the fermentation of fibers by the gut microbiota, which yields both beneficial and less favorable end-products such as short-chain fatty acids (e.g., acetate, propionate, and butyrate) that impart metabolic and immunomodulatory properties, and gases (e.g., hydrogen, carbon dioxide, and methane) that cause gastrointestinal symptoms, respectively. This narrative review summarizes (1) the implications of fibers on the gut microbiota and the pathophysiology of pediatric obesity, (2) some factors that potentially contribute to the fiber gap with an emphasis on undesirable gastrointestinal symptoms, (3) some methods to alleviate fiber-induced symptoms, and (4) the therapeutic potential of whole foods and commonly marketed fiber supplements for improved health in pediatric obesity.
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Affiliation(s)
- Nandini Basuray
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Edward C Deehan
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
- Nebraska Food for Health Center, Lincoln, NE, USA
| | - Flávio T Vieira
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Hayford M Avedzi
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Reena L Duke
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | - Hein M Tun
- JC School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Zhengxiao Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Eytan Wine
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Catherine J Field
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Andrea M Haqq
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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13
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Allaband C, Lingaraju A, Flores Ramos S, Kumar T, Javaheri H, Tiu MD, Dantas Machado AC, Richter RA, Elijah E, Haddad GG, Leone VA, Dorrestein PC, Knight R, Zarrinpar A. Time of sample collection is critical for the replicability of microbiome analyses. Nat Metab 2024; 6:1282-1293. [PMID: 38951660 PMCID: PMC11309016 DOI: 10.1038/s42255-024-01064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/08/2024] [Indexed: 07/03/2024]
Abstract
As the microbiome field moves from descriptive and associative research to mechanistic and interventional studies, being able to account for all confounding variables in the experimental design, which includes the maternal effect1, cage effect2, facility differences3, as well as laboratory and sample handling protocols4, is critical for interpretability of results. Despite significant procedural and bioinformatic improvements, unexplained variability and lack of replicability still occur. One underexplored factor is that the microbiome is dynamic and exhibits diurnal oscillations that can change microbiome composition5-7. In this retrospective analysis of 16S amplicon sequencing studies in male mice, we show that sample collection time affects the conclusions drawn from microbiome studies and its effect size is larger than those of a daily experimental intervention or dietary changes. The timing of divergence of the microbiome composition between experimental and control groups is unique to each experiment. Sample collection times as short as only 4 hours apart can lead to vastly different conclusions. Lack of consistency in the time of sample collection may explain poor cross-study replicability in microbiome research. The impact of diurnal rhythms on the outcomes and study design of other fields is unknown but likely significant.
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Affiliation(s)
- Celeste Allaband
- Division of Biomedical Sciences, University of California, San Diego, La Jolla, CA, USA
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Stephany Flores Ramos
- Division of Biomedical Sciences, University of California, San Diego, La Jolla, CA, USA
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tanya Kumar
- Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA
| | - Haniyeh Javaheri
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Maria D Tiu
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | | | - R Alexander Richter
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Emmanuel Elijah
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel G Haddad
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Hospital, San Diego, CA, USA
| | - Vanessa A Leone
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
- Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, CA, USA.
- Institute of Diabetes and Metabolic Health, University of California, San Diego, La Jolla, CA, USA.
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14
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Meloncelli N, Wilkinson SA, Rushton A, Pateman K, Gallaher S, O'Connor H, Kearney L, de Jersey S. Co-designing The Healthy Gut Diet for Preventing Gestational Diabetes: Co-design methods and process outcomes. J Hum Nutr Diet 2024. [PMID: 38894634 DOI: 10.1111/jhn.13341] [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: 02/12/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) is a common and costly condition of pregnancy. The Healthy Gut Diet for Preventing Gestational Diabetes study is a novel randomised controlled trial that aims to prevent GDM through a diet that modulates the gut microbiota for pregnant women with GDM risk factors. Despite increasing interest in co-designing interventions with consumers (lived experience experts), co-design methods and outcomes are often poorly reported. The present study aims to report on the co-design process used to develop The Healthy Gut Diet intervention. METHODS Co-design occurred across three online workshops with consumer participants (women with a lived experience of GDM, n = 11), researchers (n = 6) and workshop co-facilitators (including a consumer co-facilitator, n = 2). The workshops explored women's preferences for the mode and length of education sessions, as well as the types of information and supportive resources women wanted to receive, and undertook a "behaviour diagnosis" to understand barriers and enablers to the target behaviours (eating for gut health). The final intervention is reported according to the Template for Intervention Description and Replication. RESULTS A co-designed dietary intervention (The Healthy Gut Diet), delivered via telehealth, with a suite of educational and supportive resources that integrates published behaviour change techniques, was developed. Generally, the co-design process was reported as a positive experience based on participant feedback and evidenced by no participant dropouts over the 3-month study period. CONCLUSIONS Co-design is recognised as a process that creates a partnership between lived experience experts and researchers who can engage and empower research recipients and improve health behaviours.
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Affiliation(s)
- Nina Meloncelli
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Office of the Chief Allied Health Practitioner, Metro North Health, Herston, QLD, Australia
| | - Shelley A Wilkinson
- Department of Obstetric Medicine, Mater Mothers Hospitals, South Brisbane, QLD, Australia
- School of Pharmacy; Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alita Rushton
- Office of the Chief Allied Health Practitioner, Metro North Health, Herston, QLD, Australia
| | - Kelsey Pateman
- Centre for Allied Health Research, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- School of Dentistry, The University of Queensland, Herston, QLD, Australia
| | | | - Hannah O'Connor
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Dietetics and Foodservices; Royal Brisbane and Women's Hospital; Metro North Health, Herston, QLD, Australia
| | - Lauren Kearney
- School of Nursing, Midwifery and Social Work, The University of Queensland, Brisbane, QLD, Australia
- Women's and Newborn Service Group, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Susan de Jersey
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Dietetics and Foodservices; Royal Brisbane and Women's Hospital; Metro North Health, Herston, QLD, Australia
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15
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Grieneisen L, Hays A, Cook E, Blekhman R, Tecot S. Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type. Am J Primatol 2024:e23656. [PMID: 38873762 DOI: 10.1002/ajp.23656] [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: 06/01/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
The gut microbiome is a plastic phenotype; gut microbial composition is highly variable across an individual host's lifetime and between host social groups, and this variation has consequences for host health. However, we do not yet fully understand how longitudinal microbial dynamics and their social drivers may be influenced by ecological stressors, such as habitat degradation. Answering these questions is difficult in most wild animal systems, as it requires long-term collections of matched host, microbiome, and environmental trait data. To test if temporal and social influences on microbiome composition differ by the history of human disturbance, we leveraged banked, desiccated fecal samples collected over 5 months in 2004 from two ecologically distinct populations of wild, red-bellied lemurs (Eulemur rubriventer) that are part of a long-term study system. We found that social group explained more variation in microbiome composition than host population membership did, and that temporal variation in common microbial taxa was similar between populations, despite differences in history of human disturbance. Furthermore, we found that social group membership and collection month were both more important than individual lemur identity. Taken together, our results suggest that synchronized environments use can lead to synchronized microbial dynamics over time, even between habitats of varying quality, and that desiccated samples could become a viable approach for studying primate gut microbiota. Our work opens the door for other projects to utilize historic biological sample data sets to answer novel temporal microbiome questions in an ecological context.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, BC, Canada
| | - Allison Hays
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Erica Cook
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stacey Tecot
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
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16
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Trøseid M, Nielsen SD, Vujkovic-Cvijin I. Gut microbiome and cardiometabolic comorbidities in people living with HIV. MICROBIOME 2024; 12:106. [PMID: 38877521 PMCID: PMC11177534 DOI: 10.1186/s40168-024-01815-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Despite modern antiretroviral therapy (ART), people living with HIV (PLWH) have increased relative risk of inflammatory-driven comorbidities, including cardiovascular disease (CVD). The gut microbiome could be one of several driving factors, along with traditional risk factors and HIV-related risk factors such as coinfections, ART toxicity, and past immunodeficiency. RESULTS PLWH have an altered gut microbiome, even after adjustment for known confounding factors including sexual preference. The HIV-related microbiome has been associated with cardiometabolic comorbidities, and shares features with CVD-related microbiota profiles, in particular reduced capacity for short-chain fatty acid (SCFA) generation. Substantial inter-individual variation has so far been an obstacle for applying microbiota profiles for risk stratification. This review covers updated knowledge and recent advances in our understanding of the gut microbiome and comorbidities in PLWH, with specific focus on cardiometabolic comorbidities and inflammation. It covers a comprehensive overview of HIV-related and comorbidity-related dysbiosis, microbial translocation, and microbiota-derived metabolites. It also contains recent data from studies in PLWH on circulating metabolites related to comorbidities and underlying gut microbiota alterations, including circulating levels of the SCFA propionate, the histidine-analogue imidazole propionate, and the protective metabolite indole-3-propionic acid. CONCLUSIONS Despite recent advances, the gut microbiome and related metabolites are not yet established as biomarkers or therapeutic targets. The review gives directions for future research needed to advance the field into clinical practice, including promises and pitfalls for precision medicine. Video Abstract.
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Affiliation(s)
- Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Section for Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Susanne Dam Nielsen
- Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
- Department of Surgical Gastroenterology and Transplantation, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, Copenhagen Oe, 2100, Denmark
| | - Ivan Vujkovic-Cvijin
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Karsh Division of Gastroenterology & Hepatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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17
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Hoisington AJ, Stamper CE, Ellis JC, Lowry CA, Brenner LA. Quantifying variation across 16S rRNA gene sequencing runs in human microbiome studies. Appl Microbiol Biotechnol 2024; 108:367. [PMID: 38850297 PMCID: PMC11162379 DOI: 10.1007/s00253-024-13198-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: 02/21/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
Recent microbiome research has incorporated a higher number of samples through more participants in a study, longitudinal studies, and metanalysis between studies. Physical limitations in a sequencing machine can result in samples spread across sequencing runs. Here we present the results of sequencing nearly 1000 16S rRNA gene sequences in fecal (stabilized and swab) and oral (swab) samples from multiple human microbiome studies and positive controls that were conducted with identical standard operating procedures. Sequencing was performed in the same center across 18 different runs. The simplified mock community showed limitations in accuracy, while precision (e.g., technical variation) was robust for the mock community and actual human positive control samples. Technical variation was the lowest for stabilized fecal samples, followed by fecal swab samples, and then oral swab samples. The order of technical variation stability was inverse of DNA concentrations (e.g., highest in stabilized fecal samples), highlighting the importance of DNA concentration in reproducibility and urging caution when analyzing low biomass samples. Coefficients of variation at the genus level also followed the same trend for lower variation with higher DNA concentrations. Technical variation across both sample types and the two human sampling locations was significantly less than the observed biological variation. Overall, this research providing comparisons between technical and biological variation, highlights the importance of using positive controls, and provides semi-quantified data to better understand variation introduced by sequencing runs. KEY POINTS: • Mock community and positive control accuracy were lower than precision. • Samples with lower DNA concentration had increased technical variation across sequencing runs. • Biological variation was significantly higher than technical variation due to sequencing runs.
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Affiliation(s)
- Andrew J Hoisington
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA.
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA.
- Department of Systems Engineering and Management, Air Force Institute of Technology, Wright-Patterson Air Force Base, Dayton, OH, USA.
| | - Christopher E Stamper
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA
| | | | - Christopher A Lowry
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA
- Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, CO, USA
| | - Lisa A Brenner
- Veterans Health Administration, Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC) for Veteran Suicide Prevention, Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, CO, USA
- Department of Physical Medicine and Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, CO, USA
- Department of Psychiatry, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Nguyen NTA, Jiang Y, McQuade JL. Eating away cancer: the potential of diet and the microbiome for shaping immunotherapy outcome. Front Immunol 2024; 15:1409414. [PMID: 38873602 PMCID: PMC11169628 DOI: 10.3389/fimmu.2024.1409414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
The gut microbiome (GMB) plays a substantial role in human health and disease. From affecting gut barrier integrity to promoting immune cell differentiation, the GMB is capable of shaping host immunity and thus oncogenesis and anti-cancer therapeutic response, particularly with immunotherapy. Dietary patterns and components are key determinants of GMB composition, supporting the investigation of the diet-microbiome-immunity axis as a potential avenue to enhance immunotherapy response in cancer patients. As such, this review will discuss the role of the GMB and diet on anti-cancer immunity. We demonstrate that diet affects anti-cancer immunity through both GMB-independent and GMB-mediated mechanisms, and that different diet patterns mold the GMB's functional and taxonomic composition in distinctive ways. Dietary modulation therefore shows promise as an intervention for improving cancer outcome; however, further and more extensive research in human cancer populations is needed.
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Affiliation(s)
| | | | - Jennifer L. McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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19
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Algavi YM, Borenstein E. Relative dispersion ratios following fecal microbiota transplant elucidate principles governing microbial migration dynamics. Nat Commun 2024; 15:4447. [PMID: 38789466 PMCID: PMC11126695 DOI: 10.1038/s41467-024-48717-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: 09/12/2023] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Microorganisms frequently migrate from one ecosystem to another. Yet, despite the potential importance of this process in modulating the environment and the microbial ecosystem, our understanding of the fundamental forces that govern microbial dispersion is still lacking. Moreover, while theoretical models and in-vitro experiments have highlighted the contribution of species interactions to community assembly, identifying such interactions in vivo, specifically in communities as complex as the human gut, remains challenging. To address this gap, here we introduce a robust and rigorous computational framework, termed Relative Dispersion Ratio (RDR) analysis, and leverage data from well-characterized fecal microbiota transplant trials, to rigorously pinpoint dependencies between taxa during the colonization of human gastrointestinal tract. Our analysis identifies numerous pairwise dependencies between co-colonizing microbes during migration between gastrointestinal environments. We further demonstrate that identified dependencies agree with previously reported findings from in-vitro experiments and population-wide distribution patterns. Finally, we explore metabolic dependencies between these taxa and characterize the functional properties that facilitate effective dispersion. Collectively, our findings provide insights into the principles and determinants of community dynamics following ecological translocation, informing potential opportunities for precise community design.
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Affiliation(s)
- Yadid M Algavi
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- Faculty of Medical & Health Sciences, Tel Aviv University, Tel Aviv, Israel.
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
- Santa Fe Institute, Santa Fe, NM, USA.
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20
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Zhang S, Fang H, Hu T. fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data. Bioinformatics 2024; 40:btae314. [PMID: 38730540 PMCID: PMC11127107 DOI: 10.1093/bioinformatics/btae314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/21/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
MOTIVATION The composition and structure of microbial communities on the body surface are closely related to human health. The interaction relationship among microbes can help us understand the formation of the microecological environment and the biological mechanism by which microorganisms influence host health. With the help of high-throughput sequencing technologies, microbial abundances in a natural environment can be directly measured without the isolation of microorganisms in culture. Sequencing experiments in microbiome studies can measure the relative abundance of microbes, which is called compositional data. Although there are already many methods for correlation analysis for compositional data, the computation time or accuracy still needs to be improved for current microbiome studies. RESULTS We develop a fast and efficient algorithm, called fastCCLasso, based on a penalized weighted least squares for inferring the correlation structure of microbes from compositional data in microbiome studies. We perform a large number of numerical experiments and the simulation results show that fastCCLasso outperforms its competitors in edge detection for inferring the correlation network. We also apply fastCCLasso for estimating microbial networks in microbiome studies and fastCCLasso provides a conservative network with comparable false discovery counts that are derived from shuffled data. AVAILABILITY AND IMPLEMENTATION FastCCLasso is open source and freely available from https://github.com/ShenZhang-Statistics/fastCCLasso under GNU LGPL v3.
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Affiliation(s)
- Shen Zhang
- School of Mathematical Sciences, Capital Normal University, Beijing 100048, China
| | - Huaying Fang
- Beijing Advanced Innovation Center for Imaging Theory and Technology, Capital Normal University, Beijing 100048, China
- Academy for Multidisciplinary Studies, Capital Normal University, Beijing 100048, China
| | - Tao Hu
- School of Mathematical Sciences, Capital Normal University, Beijing 100048, China
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21
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Deehan EC, Mocanu V, Madsen KL. Effects of dietary fibre on metabolic health and obesity. Nat Rev Gastroenterol Hepatol 2024; 21:301-318. [PMID: 38326443 DOI: 10.1038/s41575-023-00891-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/09/2024]
Abstract
Obesity and metabolic syndrome represent a growing epidemic worldwide. Body weight is regulated through complex interactions between hormonal, neural and metabolic pathways and is influenced by numerous environmental factors. Imbalances between energy intake and expenditure can occur due to several factors, including alterations in eating behaviours, abnormal satiation and satiety, and low energy expenditure. The gut microbiota profoundly affects all aspects of energy homeostasis through diverse mechanisms involving effects on mucosal and systemic immune, hormonal and neural systems. The benefits of dietary fibre on metabolism and obesity have been demonstrated through mechanistic studies and clinical trials, but many questions remain as to how different fibres are best utilized in managing obesity. In this Review, we discuss the physiochemical properties of different fibres, current findings on how fibre and the gut microbiota interact to regulate body weight homeostasis, and knowledge gaps related to using dietary fibres as a complementary strategy. Precision medicine approaches that utilize baseline microbiota and clinical characteristics to predict individual responses to fibre supplementation represent a new paradigm with great potential to enhance weight management efficacy, but many challenges remain before these approaches can be fully implemented.
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Affiliation(s)
- Edward C Deehan
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
- Nebraska Food for Health Center, Lincoln, NE, USA
| | - Valentin Mocanu
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
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22
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Zhang J, Qi H, Li M, Wang Z, Jia X, Sun T, Du S, Su C, Zhi M, Du W, Ouyang Y, Wang P, Huang F, Jiang H, Li L, Bai J, Wei Y, Zhang X, Wang H, Zhang B, Feng Q. Diet Mediate the Impact of Host Habitat on Gut Microbiome and Influence Clinical Indexes by Modulating Gut Microbes and Serum Metabolites. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310068. [PMID: 38477427 PMCID: PMC11109649 DOI: 10.1002/advs.202310068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/04/2024] [Indexed: 03/14/2024]
Abstract
The impact of external factors on the human gut microbiota and how gut microbes contribute to human health is an intriguing question. Here, the gut microbiome of 3,224 individuals (496 with serum metabolome) with 109 variables is studied. Multiple analyses reveal that geographic factors explain the greatest variance of the gut microbiome and the similarity of individuals' gut microbiome is negatively correlated with their geographic distance. Main food components are the most important factors that mediate the impact of host habitats on the gut microbiome. Diet and gut microbes collaboratively contribute to the variation of serum metabolites, and correlate to the increase or decrease of certain clinical indexes. Specifically, systolic blood pressure is lowered by vegetable oil through increasing the abundance of Blautia and reducing the serum level of 1-palmitoyl-2-palmitoleoyl-GPC (16:0/16:1), but it is reduced by fruit intake through increasing the serum level of Blautia improved threonate. Besides, aging-related clinical indexes are also closely correlated with the variation of gut microbes and serum metabolites. In this study, the linkages of geographic locations, diet, the gut microbiome, serum metabolites, and physiological indexes in a Chinese population are characterized. It is proved again that gut microbes and their metabolites are important media for external factors to affect human health.
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Affiliation(s)
- Jiguo Zhang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Houbao Qi
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Meihui Li
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Zhihong Wang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Xiaofang Jia
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Tianyong Sun
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Shufa Du
- Department of NutritionGillings School of Global Public HealthUniversity of North Carolina at Chapel HillChapel HillNC27599USA
| | - Chang Su
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Mengfan Zhi
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Wenwen Du
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Yifei Ouyang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Pingping Wang
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
| | - Feifei Huang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Hongru Jiang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Li Li
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Jing Bai
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Yanli Wei
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Xiaofan Zhang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Huijun Wang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Bing Zhang
- National Institute for Nutrition and HealthChinese Center for Disease Control and PreventionBeijing100050China
- Key Laboratory of Trace Element NutritionNational Health CommissionBeijing100050China
| | - Qiang Feng
- Department of Human MicrobiomeSchool and Hospital of StomatologyCheeloo College of MedicineSD University & SD Key Laboratory of Oral Tissue Regeneration & SD Engineering Laboratory for Dental Materials and Oral Tissue RegenerationJinan250012China
- State key laboratory of microbial technologySD UniversityQingdao266237China
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23
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McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol 2024; 42:715-718. [PMID: 37500913 PMCID: PMC10818020 DOI: 10.1038/s41587-023-01845-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/25/2023] [Indexed: 07/29/2023]
Abstract
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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Affiliation(s)
- Daniel McDonald
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - James T Morton
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Giorgia Nicolaou
- Halicioglu Data Science Institute, University of California San Diego, La Jolla, CA, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Søren M Karst
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Todd DeSantis
- Department of Informatics, Second Genome, Brisbane, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Andrew Bartko
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Aki S Havulinna
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
| | | | - Susan Cheng
- Division of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare, Helsinki, Finland
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Mohit Jain
- Sapient Bioanalytics, LLC, San Diego, CA, USA
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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24
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Whiteoak B, Dawson SL, Callaway L, de Jersey S, Eley V, Evans J, Kothari A, Navarro S, Gallegos D. Food Insecurity Is Associated with Diet Quality in Pregnancy: A Cross-Sectional Study. Nutrients 2024; 16:1319. [PMID: 38732568 PMCID: PMC11085356 DOI: 10.3390/nu16091319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Household food insecurity (HFI) and poorer prenatal diet quality are both associated with adverse perinatal outcomes. However, research assessing the relationship between HFI and diet quality in pregnancy is limited. A cross-sectional online survey was conducted to examine the relationship between HFI and diet quality among 1540 pregnant women in Australia. Multiple linear regression models were used to examine the associations between HFI severity (marginal, low, and very low food security compared to high food security) and diet quality and variety, adjusting for age, education, equivalised household income, and relationship status. Logistic regression models were used to assess the associations between HFI and the odds of meeting fruit and vegetable recommendations, adjusting for education. Marginal, low, and very low food security were associated with poorer prenatal diet quality (adj β = -1.9, -3.6, and -5.3, respectively; p < 0.05), and very low food security was associated with a lower dietary variety (adj β = -0.5, p < 0.001). An association was also observed between HFI and lower odds of meeting fruit (adjusted odds ratio [AOR]: 0.61, 95% CI: 0.49-0.76, p < 0.001) and vegetable (AOR: 0.40, 95% CI: 0.19-0.84, p = 0.016) recommendations. Future research should seek to understand what policy and service system changes are required to reduce diet-related disparities in pregnancy.
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Affiliation(s)
- Bree Whiteoak
- School of Exercise and Nutrition Sciences, Faculty of Health, Queensland University of Technology (QUT), 149 Victoria Park Road, Kelvin Grove, QLD 4059, Australia;
- Centre for Childhood Nutrition Research, Faculty of Health, Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD 4101, Australia;
- QIMR Berghofer Medical Research Institute, 300 Herston Rd., Herston, QLD 4006, Australia
| | - Samantha L. Dawson
- Food & Mood Centre, IMPACT—The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Barwon Health, Deakin University, Geelong, VIC 3220, Australia;
| | - Leonie Callaway
- Women’s and Newborns Services, Royal Brisbane and Women’s Hospital, Herston, QLD 4006, Australia;
- Faculty of Medicine, The University of Queensland, 288 Herston Rd., Herston, QLD 4006, Australia; (V.E.); (A.K.)
| | - Susan de Jersey
- Department of Dietetics and Foodservices, Royal Brisbane and Women’s Hospital, Herston, QLD 4006, Australia;
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, 288 Herston Rd., Herston, QLD 4006, Australia
| | - Victoria Eley
- Faculty of Medicine, The University of Queensland, 288 Herston Rd., Herston, QLD 4006, Australia; (V.E.); (A.K.)
- Department of Anaesthesia and Perioperative Medicine, Royal Brisbane and Women’s Hospital, Herston, QLD 4006, Australia
| | - Joanna Evans
- Maternity Services, Caboolture Hospital, McKean Street, Caboolture, QLD 4510, Australia;
| | - Alka Kothari
- Faculty of Medicine, The University of Queensland, 288 Herston Rd., Herston, QLD 4006, Australia; (V.E.); (A.K.)
- Redcliffe Hospital, Anzac Avenue, Redcliffe, QLD 4020, Australia
| | - Severine Navarro
- Centre for Childhood Nutrition Research, Faculty of Health, Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD 4101, Australia;
- QIMR Berghofer Medical Research Institute, 300 Herston Rd., Herston, QLD 4006, Australia
- Faculty of Medicine, The University of Queensland, 288 Herston Rd., Herston, QLD 4006, Australia; (V.E.); (A.K.)
| | - Danielle Gallegos
- School of Exercise and Nutrition Sciences, Faculty of Health, Queensland University of Technology (QUT), 149 Victoria Park Road, Kelvin Grove, QLD 4059, Australia;
- Centre for Childhood Nutrition Research, Faculty of Health, Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD 4101, Australia;
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25
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Saadh MJ, Ahmed HM, Alani ZK, Al Zuhairi RAH, Almarhoon ZM, Ahmad H, Ubaid M, Alwan NH. The Role of Gut-derived Short-Chain Fatty Acids in Multiple Sclerosis. Neuromolecular Med 2024; 26:14. [PMID: 38630350 DOI: 10.1007/s12017-024-08783-4] [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: 02/04/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024]
Abstract
Multiple sclerosis (MS) is a chronic condition affecting the central nervous system (CNS), where the interplay of genetic and environmental factors influences its pathophysiology, triggering immune responses and instigating inflammation. Contemporary research has been notably dedicated to investigating the contributions of gut microbiota and their metabolites in modulating inflammatory reactions within the CNS. Recent recognition of the gut microbiome and dietary patterns as environmental elements impacting MS development emphasizes the potential influence of small, ubiquitous molecules from microbiota, such as short-chain fatty acids (SCFAs). These molecules may serve as vital molecular signals or metabolic substances regulating host cellular metabolism in the intricate interplay between microbiota and the host. A current emphasis lies on optimizing the health-promoting attributes of colonic bacteria to mitigate urinary tract issues through dietary management. This review aims to spotlight recent investigations on the impact of SCFAs on immune cells pivotal in MS, the involvement of gut microbiota and SCFAs in MS development, and the considerable influence of probiotics on gastrointestinal disruptions in MS. Comprehending the gut-CNS connection holds promise for the development of innovative therapeutic approaches, particularly probiotic-based supplements, for managing MS.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | - Hani Moslem Ahmed
- Department of Dental Industry Techniques, Al-Noor University College, Nineveh, Iraq
| | - Zaid Khalid Alani
- College of Health and Medical Technical, Al-Bayan University, Baghdad, Iraq
| | | | - Zainab M Almarhoon
- Department of Chemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Hijaz Ahmad
- Section of Mathematics, International Telematic University Uninettuno, Corso Vittorio Emanuele II, 39, 00186, Rome, Italy.
- Center for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Mubarak Al-Abdullah, Kuwait.
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon.
| | - Mohammed Ubaid
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
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26
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Sarrazin-Gendron R, Ghasemloo Gheidari P, Butyaev A, Keding T, Cai E, Zheng J, Mutalova R, Mounthanyvong J, Zhu Y, Nazarova E, Drogaris C, Erhart K, Brouillette A, Richard G, Pitchford R, Caisse S, Blanchette M, McDonald D, Knight R, Szantner A, Waldispühl J. Improving microbial phylogeny with citizen science within a mass-market video game. Nat Biotechnol 2024:10.1038/s41587-024-02175-6. [PMID: 38622344 DOI: 10.1038/s41587-024-02175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 02/05/2024] [Indexed: 04/17/2024]
Abstract
Citizen science video games are designed primarily for users already inclined to contribute to science, which severely limits their accessibility for an estimated community of 3 billion gamers worldwide. We created Borderlands Science (BLS), a citizen science activity that is seamlessly integrated within a popular commercial video game played by tens of millions of gamers. This integration is facilitated by a novel game-first design of citizen science games, in which the game design aspect has the highest priority, and a suitable task is then mapped to the game design. BLS crowdsources a multiple alignment task of 1 million 16S ribosomal RNA sequences obtained from human microbiome studies. Since its initial release on 7 April 2020, over 4 million players have solved more than 135 million science puzzles, a task unsolvable by a single individual. Leveraging these results, we show that our multiple sequence alignment simultaneously improves microbial phylogeny estimations and UniFrac effect sizes compared to state-of-the-art computational methods. This achievement demonstrates that hyper-gamified scientific tasks attract massive crowds of contributors and offers invaluable resources to the scientific community.
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Affiliation(s)
| | | | | | - Timothy Keding
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Eddie Cai
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Jiayue Zheng
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Renata Mutalova
- School of Computer Science, McGill University, Montréal, QC, Canada
| | | | - Yuxue Zhu
- School of Computer Science, McGill University, Montréal, QC, Canada
| | - Elena Nazarova
- School of Computer Science, McGill University, Montréal, QC, Canada
| | | | - Kornél Erhart
- Massively Multiplayer Online Science, Gryon, Switzerland
| | | | | | | | | | | | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Attila Szantner
- School of Computer Science, McGill University, Montréal, QC, Canada
- Massively Multiplayer Online Science, Gryon, Switzerland
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montréal, QC, Canada.
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27
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Mandal S, Kim DH, Hua X, Li S, Shi J. Estimating the overall fraction of phenotypic variance attributed to high-dimensional predictors measured with error. Biostatistics 2024; 25:486-503. [PMID: 36797830 PMCID: PMC11017132 DOI: 10.1093/biostatistics/kxad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
In prospective genomic studies (e.g., DNA methylation, metagenomics, and transcriptomics), it is crucial to estimate the overall fraction of phenotypic variance (OFPV) attributed to the high-dimensional genomic variables, a concept similar to heritability analyses in genome-wide association studies (GWAS). Unlike genetic variants in GWAS, these genomic variables are typically measured with error due to technical limitation and temporal instability. While the existing methods developed for GWAS can be used, ignoring measurement error may severely underestimate OFPV and mislead the design of future studies. Assuming that measurement error variances are distributed similarly between causal and noncausal variables, we show that the asymptotic attenuation factor equals to the average intraclass correlation coefficients of all genomic variables, which can be estimated based on a pilot study with repeated measurements. We illustrate the method by estimating the contribution of microbiome taxa to body mass index and multiple allergy traits in the American Gut Project. Finally, we show that measurement error does not cause meaningful bias when estimating the correlation of effect sizes for two traits.
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Affiliation(s)
- Soutrik Mandal
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - Do Hyun Kim
- Department of Biostatistics, Fielding School of Public Health, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Xing Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Shilan Li
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, USA
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28
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Petrone BL, Bartlett A, Jiang S, Korenek A, Vintila S, Tenekjian C, Yancy WS, David LA, Kleiner M. Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.09.588275. [PMID: 38645092 PMCID: PMC11030321 DOI: 10.1101/2024.04.09.588275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin or hair, but detection of consumed foods in stool has also been shown to be possible via DNA sequencing. An additional food macromolecule in stool that harbors sequence information is protein. However, the use of protein as an intake biomarker has only been explored to a very limited extent. Here, we evaluate and compare measurement of residual food-derived DNA and protein in stool as potential biomarkers of intake. We performed a pilot study of DNA sequencing-based metabarcoding (FoodSeq) and mass spectrometry-based metaproteomics in five individuals' stool sampled in short, longitudinal bursts accompanied by detailed diet records (n=27 total samples). Dietary data provided by stool DNA, stool protein, and written diet record independently identified a strong within-person dietary signature, identified similar food taxa, and had significantly similar global structure in two of the three pairwise comparisons between measurement techniques (DNA-to-protein and DNA-to-diet record). Metaproteomics identified proteins including myosin, ovalbumin, and beta-lactoglobulin that differentiated food tissue types like beef from dairy and chicken from egg, distinctions that were not possible by DNA alone. Overall, our results lay the groundwork for development of targeted metaproteomic assays for dietary assessment and demonstrate that diverse molecular components of food can be leveraged to study food intake using stool samples.
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Affiliation(s)
- Brianna L Petrone
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC, United States
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Abigail Korenek
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | | | - William S Yancy
- Duke Lifestyle and Weight Management Center, Durham, NC, United States
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Brennan C, Chan K, Kumar T, Maissy E, Brubaker L, Dothard MI, Gilbert JA, Gilbert KE, Lewis AL, Thackray VG, Zarrinpar A, Knight R. Harnessing the power within: engineering the microbiome for enhanced gynecologic health. REPRODUCTION AND FERTILITY 2024; 5:e230060. [PMID: 38513356 PMCID: PMC11046331 DOI: 10.1530/raf-23-0060] [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: 12/28/2023] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
Abstract Although numerous studies have demonstrated the impact of microbiome manipulation on human health, research on the microbiome's influence on female health remains relatively limited despite substantial disease burden. In light of this, we present a selected review of clinical trials and preclinical studies targeting both the vaginal and gut microbiomes for the prevention or treatment of various gynecologic conditions. Specifically, we explore studies that leverage microbiota transplants, probiotics, prebiotics, diet modifications, and engineered microbial strains. A healthy vaginal microbiome for females of reproductive age consists of lactic acid-producing bacteria predominantly of the Lactobacillus genus, which serves as a protective barrier against pathogens and maintains a balanced ecosystem. The gut microbiota's production of short-chain fatty acids, metabolism of primary bile acids, and modulation of sex steroid levels have significant implications for the interplay between host and microbes throughout the body, ultimately impacting reproductive health. By harnessing interventions that modulate both the vaginal and gut microbiomes, it becomes possible to not only maintain homeostasis but also mitigate pathological conditions. While the field is still working toward making broad clinical recommendations, the current studies demonstrate that manipulating the microbiome holds great potential for addressing diverse gynecologic conditions. Lay summary Manipulating the microbiome has recently entered popular culture, with various diets thought to aid the microbes that live within us. These microbes live in different locations of our body and accordingly help us digest food, modulate our immune system, and influence reproductive health. The role of the microbes living in and influencing the female reproductive tract remains understudied despite known roles in common conditions such as vulvovaginal candidiasis (affecting 75% of females in their lifetime), bacterial vaginosis (25% of females in their lifetime), cervical HPV infection (80% of females in their lifetime), endometriosis (6-10% of females of reproductive age), and polycystic ovary syndrome (10-12% of females of reproductive age). Here, we review four different approaches used to manipulate the female reproductive tract and gastrointestinal system microbiomes: microbiota transplants, probiotics, prebiotics, and dietary interventions, and the use of engineered microbial strains. In doing so, we aim to stimulate discussion on new ways to understand and treat female reproductive health conditions.
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Affiliation(s)
- Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Kristina Chan
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Tanya Kumar
- Medical Scientist Training Program, University of California San Diego, La Jolla, California, USA
| | - Erica Maissy
- Division of Gastroenterology, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Linda Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Marisol I Dothard
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Katharine E Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amanda L Lewis
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Varykina G Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Amir Zarrinpar
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, California, USA
- Division of Gastroenterology, University of California San Diego, La Jolla, California, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, California, USA
- Institute of Diabetes and Metabolic Health, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California, USA
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Ribeiro MC, Levi Y, Moraschini V, Messora MR, Furlaneto FAC. Effects of Prebiotic Therapy on Gastrointestinal Microbiome of Individuals with Different Inflammatory Conditions: A Systematic Review of Randomized Controlled Trials. Probiotics Antimicrob Proteins 2024; 16:673-695. [PMID: 37093515 DOI: 10.1007/s12602-023-10075-5] [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] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Prebiotics are substrates selectively utilized by host microorganisms conferring a health benefit. The effects of prebiotics on the gut microbiome of individuals with inflammatory processes need further investigations. The purpose of this study was to evaluate the effects of prebiotics on the gastrointestinal microbiome of individuals with some types of inflammatory conditions. Randomized controlled clinical trials (RCTs) evaluating the effects of different prebiotics on the gut microbiome were included. A systematic review of the literature including searches in PubMed/MEDLINE, EMBASE, Cochrane Library, Web of Science, and Scopus databases was performed until 23 March 2023. The risk of bias was assessed using the Cochrane Collaboration's criteria. Qualitative data was tabulated to facilitate comparisons and represented in the form of descriptive statistics and summary tables. Thirty trials, ranging from 12 to 135 patients, were included. The most commonly used prebiotic type was inulin-type fructans, and the treatment duration ranged from 1 to 36 weeks. The majority of the trials investigated the gut microbiome using 16 s rRNA gene sequencing on the Illumina Miseq platform. In general, prebiotic therapy exerted positive effects on inflammatory conditions. An increase in Bifidobacterium genus was the most common shift in bacterial composition observed. Within the limits of this systematic review, it can be suggested that prebiotic therapy presents the potential to favorably modulate the gastrointestinal microbiome of individuals with different types of inflammatory conditions.
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Affiliation(s)
- M C Ribeiro
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil
| | - Ylas Levi
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil
| | - V Moraschini
- Department of Periodontology, Dental Research Division, School of Dentistry, Veiga de Almeida University, Rio de Janeiro, Brazil
| | - M R Messora
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil
| | - F A C Furlaneto
- Department of Oral Surgery and Periodontology, School of Dentistry of Ribeirao Preto, University of Sao Paulo - USP, Av. Café S/N, 14020-150, Ribeirao Preto, São Paulo, Brazil.
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31
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Shea MK, Strath L, Kim M, Ðoàn LN, Booth SL, Brinkley TE, Kritchevsky SB. Perspective: Promoting Healthy Aging through Nutrition: A Research Centers Collaborative Network Workshop Report. Adv Nutr 2024; 15:100199. [PMID: 38432592 PMCID: PMC10965474 DOI: 10.1016/j.advnut.2024.100199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024] Open
Abstract
Within 20 y, the number of adults in the United States over the age of 65 y is expected to more than double and the number over age 85 y is expected to more than triple. The risk for most chronic diseases and disabilities increases with age, so this demographic shift carries significant implications for the individual, health care providers, and population health. Strategies that delay or prevent the onset of age-related diseases are becoming increasingly important. Although considerable progress has been made in understanding the contribution of nutrition to healthy aging, it has become increasingly apparent that much remains to be learned, especially because the aging process is highly variable. Most federal nutrition programs and nutrition research studies define all adults over age 65 y as "older" and do not account for physiological and metabolic changes that occur throughout older adulthood that influence nutritional needs. Moreover, the older adult population is becoming more racially and ethnically diverse, so cultural preferences and other social determinants of health need to be considered. The Research Centers Collaborative Network sponsored a 1.5-d multidisciplinary workshop that included sessions on dietary patterns in health and disease, timing and targeting interventions, and health disparities and the social context of diet and food choice. The agenda and presentations can be found at https://www.rccn-aging.org/nutrition-2023-rccn-workshop. Here we summarize the workshop's themes and discussions and highlight research gaps that if filled will considerably advance our understanding of the role of nutrition in healthy aging.
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Affiliation(s)
- M Kyla Shea
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States.
| | - Larissa Strath
- College of Medicine, Department of Health Outcomes and Biomedical Informatics, the University of Florida, Gainesville, FL, United States; Clinical and Translational Science Institute, Pain Research and Intervention Center of Excellence, the University of Florida, Gainesville, FL, United States
| | - Minjee Kim
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States; Institute of Public Health Medicine, Center for Applied Health Research on Aging, Northwestern University Feinberg School of Medicine, Chicago, IL, United States; Center for Circadian and Sleep Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lan N Ðoàn
- Department for Population Health, Section for Health Equity, New York University Grossman School of Medicine, New York, NY, United States
| | - Sarah L Booth
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
| | - Tina E Brinkley
- Department of Gerontology and Geriatric Medicine, Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Stephen B Kritchevsky
- Department of Gerontology and Geriatric Medicine, Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, NC, United States
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Dilmore AH, Kuplicki R, McDonald D, Kumar M, Estaki M, Youngblut N, Tyakht A, Ackermann G, Blach C, MahmoudianDehkordi S, Dunlop BW, Bhattacharyya S, Guinjoan S, Mandaviya P, Ley RE, Kaddaruh-Dauok R, Paulus MP, Knight R. Medication Use is Associated with Distinct Microbial Features in Anxiety and Depression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585820. [PMID: 38562901 PMCID: PMC10983923 DOI: 10.1101/2024.03.19.585820] [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
This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive disorder (MDD), as defined by DSM-IV or V criteria. The study also examined the influence of medication use, particularly antidepressants and/or anxiolytics, classified through the Anatomical Therapeutic Chemical (ATC) Classification System, on the gut microbiota. Both 16S rRNA gene amplicon sequencing and shallow shotgun sequencing were performed on DNA extracted from 666 fecal samples from the Tulsa-1000 and NeuroMAP CoBRE cohorts. The results highlight the significant influence of medication use; antidepressant use is associated with significant differences in gut microbiota beta diversity and has a larger effect size than NPD diagnosis. Next, specific microbes were associated with ANXD and MDD, highlighting their potential for non-pharmacological intervention. Finally, the study demonstrated the capability of Random Forest classifiers to predict diagnoses of NPD and medication use from microbial profiles, suggesting a promising direction for the use of gut microbiota as biomarkers for NPD. The findings suggest that future research on the gut microbiota's role in NPD and its interactions with pharmacological treatments are needed.
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Affiliation(s)
- Amanda Hazel Dilmore
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Rayus Kuplicki
- Laureate Institute for Brain Research, Tulsa, Oklahoma, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Megha Kumar
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Mehrbod Estaki
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Nicholas Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Alexander Tyakht
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Colette Blach
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Boadie W. Dunlop
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Sudeepa Bhattacharyya
- Department of Biological Sciences, Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR, USA
| | | | - Pooja Mandaviya
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Rima Kaddaruh-Dauok
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Duke Institute of Brain Sciences, Duke University, Durham, North Carolina, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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33
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Ahn S, Datta S. Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values. BMC Bioinformatics 2024; 25:117. [PMID: 38500042 PMCID: PMC10946111 DOI: 10.1186/s12859-024-05689-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 02/02/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND A recent breakthrough in differential network (DN) analysis of microbiome data has been realized with the advent of next-generation sequencing technologies. The DN analysis disentangles the microbial co-abundance among taxa by comparing the network properties between two or more graphs under different biological conditions. However, the existing methods to the DN analysis for microbiome data do not adjust for other clinical differences between subjects. RESULTS We propose a Statistical Approach via Pseudo-value Information and Estimation for Differential Network Analysis (SOHPIE-DNA) that incorporates additional covariates such as continuous age and categorical BMI. SOHPIE-DNA is a regression technique adopting jackknife pseudo-values that can be implemented readily for the analysis. We demonstrate through simulations that SOHPIE-DNA consistently reaches higher recall and F1-score, while maintaining similar precision and accuracy to existing methods (NetCoMi and MDiNE). Lastly, we apply SOHPIE-DNA on two real datasets from the American Gut Project and the Diet Exchange Study to showcase the utility. The analysis of the Diet Exchange Study is to showcase that SOHPIE-DNA can also be used to incorporate the temporal change of connectivity of taxa with the inclusion of additional covariates. As a result, our method has found taxa that are related to the prevention of intestinal inflammation and severity of fatigue in advanced metastatic cancer patients. CONCLUSION SOHPIE-DNA is the first attempt of introducing the regression framework for the DN analysis in microbiome data. This enables the prediction of characteristics of a connectivity of a network with the presence of additional covariate information in the regression. The R package with a vignette of our methodology is available through the CRAN repository ( https://CRAN.R-project.org/package=SOHPIE ), named SOHPIE (pronounced as Sofie). The source code and user manual can be found at https://github.com/sjahnn/SOHPIE-DNA .
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Affiliation(s)
- Seungjun Ahn
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Somnath Datta
- Department of Biostatistics, University of Florida, Gainesville, FL, USA.
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Johnson-Martínez JP, Diener C, Levine AE, Wilmanski T, Suskind DL, Ralevski A, Hadlock J, Magis AT, Hood L, Rappaport N, Gibbons SM. Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with reduced kidney function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.04.531100. [PMID: 36945445 PMCID: PMC10028848 DOI: 10.1101/2023.03.04.531100] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Bowel movement frequency (BMF) has been linked to changes in the composition of the human gut microbiome and to many chronic conditions, like metabolic disorders, neurodegenerative diseases, chronic kidney disease (CKD), and other intestinal pathologies like irritable bowel syndrome and inflammatory bowel disease. Lower BMF (constipation) can lead to compromised intestinal barrier integrity and a switch from saccharolytic to proteolytic fermentation within the microbiota, giving rise to microbially-derived toxins that may make their way into circulation and cause damage to organ systems. However, the connections between BMF, gut microbial metabolism, and the early-stage development and progression of chronic disease remain underexplored. Here, we examined the phenotypic impact of BMF variation in a cohort of generally-healthy, community dwelling adults with detailed clinical, lifestyle, and multi-omic data. We showed significant differences in microbially-derived blood plasma metabolites, gut bacterial genera, clinical chemistries, and lifestyle factors across BMF groups that have been linked to inflammation, cardiometabolic health, liver function, and CKD severity and progression. We found that the higher plasma levels of 3-indoxyl sulfate (3-IS), a microbially-derived metabolite associated with constipation, was in turn negatively associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. Causal mediation analysis revealed that the effect of BMF on eGFR was significantly mediated by 3-IS. Finally, we identify self-reported diet, lifestyle, and psychological factors associated with BMF variation, which indicate several common-sense strategies for mitigating constipation and diarrhea. Overall, we suggest that aberrant BMF is an underappreciated risk factor in the development of chronic diseases, even in otherwise healthy populations.
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Affiliation(s)
- Johannes P. Johnson-Martínez
- Institute for Systems Biology, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | | | - Anne E. Levine
- Institute for Systems Biology, Seattle, WA 98109, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | | | | | | | | | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Phenome Health, Seattle, WA 98109
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Noa Rappaport
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Sean M. Gibbons
- Institute for Systems Biology, Seattle, WA 98109, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- eScience Institute, University of Washington, Seattle, WA 98195, USA
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35
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Luan T, Cepeda V, Liu B, Bowen Z, Ayyangar U, Almeida M, Hill CM, Koren S, Treangen TJ, Porter A, Pop M. MetaCompass: Reference-guided Assembly of Metagenomes. ARXIV 2024:arXiv:2403.01578v1. [PMID: 38903742 PMCID: PMC11188144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here we describe the first effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available.
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Affiliation(s)
- Tu Luan
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Victoria Cepeda
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Bo Liu
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Zac Bowen
- Fraunhofer USA Center Mid-Atlantic, Riverdale, Maryland, USA
| | - Ujjwal Ayyangar
- Fraunhofer USA Center Mid-Atlantic, Riverdale, Maryland, USA
| | - Mathieu Almeida
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Christopher M. Hill
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Todd J. Treangen
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Adam Porter
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
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Wilkinson JL, Thornhill I, Oldenkamp R, Gachanja A, Busquets R. Pharmaceuticals and Personal Care Products in the Aquatic Environment: How Can Regions at Risk be Identified in the Future? ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:575-588. [PMID: 37818878 DOI: 10.1002/etc.5763] [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: 05/16/2023] [Revised: 07/11/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023]
Abstract
Pharmaceuticals and personal care products (PPCPs) are an indispensable component of a healthy society. However, they are well-established environmental contaminants, and many can elicit biological disruption in exposed organisms. It is now a decade since the landmark review covering the top 20 questions on PPCPs in the environment (Boxall et al., 2012). In the present study we discuss key research priorities for the next 10 years with a focus on how regions where PPCPs pose the greatest risk to environmental and human health, either now or in the future, can be identified. Specifically, we discuss why this problem is of importance and review our current understanding of PPCPs in the aquatic environment. Foci include PPCP occurrence and what drives their environmental emission as well as our ability to both quantify and model their distribution. We highlight critical areas for future research including the involvement of citizen science for environmental monitoring and using modeling techniques to bridge the gap between research capacity and needs. Because prioritization of regions in need of environmental monitoring is needed to assess future/current risks, we also propose four criteria with which this may be achieved. By applying these criteria to available monitoring data, we narrow the focus on where monitoring efforts for PPCPs are most urgent. Specifically, we highlight 19 cities across Africa, Central America, the Caribbean, and Asia as priorities for future environmental monitoring and risk characterization and define four priority research questions for the next 10 years. Environ Toxicol Chem 2024;43:575-588. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- John L Wilkinson
- Environment and Geography Department, University of York, York, UK
| | - Ian Thornhill
- School of Environment, Education and Development, The University of Manchester, Manchester, UK
| | - Rik Oldenkamp
- Amsterdam Institute for Life and Environment, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, The Netherlands
| | - Anthony Gachanja
- Department of Food Science and Post-Harvest Technology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Rosa Busquets
- Department of Chemical and Pharmaceutical Sciences, Kingston University London, Kingston-upon-Thames, UK
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37
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Burcham ZM, Belk AD, McGivern BB, Bouslimani A, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel HL, Xu ZZ, Nieciecki V, Zhu Q, Shaffer M, Panitchpakdi M, Weldon KC, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Chan SHJ, Connor M, Boyd D, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Dorrestein PC, Wrighton KC, Carter DO, Knight R, Metcalf JL. A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nat Microbiol 2024; 9:595-613. [PMID: 38347104 PMCID: PMC10914610 DOI: 10.1038/s41564-023-01580-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/08/2023] [Indexed: 03/07/2024]
Abstract
Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.
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Affiliation(s)
- Zachary M Burcham
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Aeriel D Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Animal Sciences, Auburn University, Auburn, AL, USA
| | - Bridget B McGivern
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Parsa Ghadermazi
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA
- Institute for Systems Genetics, New York Grossman School of Medicine, New York University, New York, NY, USA
- Department of Computer Science, New York University, New York, NY, USA
| | - Anru R Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Pixu Shi
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Alexandra Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Heather L Deel
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhenjiang Zech Xu
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Victoria Nieciecki
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Weldon
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kalen Cantrell
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, CO, USA
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, Moab, UT, USA
| | - Greg C Humphry
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Siu Hung Joshua Chan
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - Melissa Connor
- Forensic Investigation Research Station, Colorado Mesa University, Grand Junction, CO, USA
| | - Derek Boyd
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Department of Social, Cultural, and Justice Studies, University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Jake Smith
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
- Mid-America College of Funeral Service, Jeffersonville, IN, USA
| | - Jenna M S Watson
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Giovanna Vidoli
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Dawnie Steadman
- Forensic Anthropology Center, Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Aaron M Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - David O Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, HI, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA.
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
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Jacquier EF, van de Wouw M, Nekrasov E, Contractor N, Kassis A, Marcu D. Local and Systemic Effects of Bioactive Food Ingredients: Is There a Role for Functional Foods to Prime the Gut for Resilience? Foods 2024; 13:739. [PMID: 38472851 DOI: 10.3390/foods13050739] [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: 01/12/2024] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Scientific advancements in understanding the impact of bioactive components in foods on the gut microbiota and wider physiology create opportunities for designing targeted functional foods. The selection of bioactive ingredients with potential local or systemic effects holds promise for influencing overall well-being. An abundance of studies demonstrate that gut microbiota show compositional changes that correlate age and disease. However, navigating this field, especially for non-experts, remains challenging, given the abundance of bioactive ingredients with varying levels of scientific substantiation. This narrative review addresses the current knowledge on the potential impact of the gut microbiota on host health, emphasizing gut microbiota resilience. It explores evidence related to the extensive gut health benefits of popular dietary components and bioactive ingredients, such as phytochemicals, fermented greens, fibres, prebiotics, probiotics, and postbiotics. Importantly, this review distinguishes between the potential local and systemic effects of both popular and emerging ingredients. Additionally, it highlights how dietary hormesis promotes gut microbiota resilience, fostering better adaptation to stress-a hallmark of health. By integrating examples of bioactives, this review provides insights to guide the design of evidence-based functional foods aimed at priming the gut for resilience.
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Affiliation(s)
| | - Marcel van de Wouw
- Department of Pediatrics, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | | | - Amira Kassis
- Neat Science, 1618 Chatel-Saint-Denis, Switzerland
| | - Diana Marcu
- School of Molecular Biosciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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Humińska-Lisowska K, Zielińska K, Mieszkowski J, Michałowska-Sawczyn M, Cięszczyk P, Łabaj PP, Wasąg B, Frączek B, Grzywacz A, Kochanowicz A, Kosciolek T. Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study. PLoS One 2024; 19:e0297858. [PMID: 38381714 PMCID: PMC10880968 DOI: 10.1371/journal.pone.0297858] [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: 06/14/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024] Open
Abstract
The influence of human gut microbiota on health and disease is now commonly appreciated. Therefore, it is not surprising that microbiome research has found interest in the sports community, hoping to improve health and optimize performance. Comparative studies found new species or pathways that were more enriched in elites than sedentary controls. In addition, sport-specific and performance-level-specific microbiome features have been identified. However, the results remain inconclusive and indicate the need for further assessment. In this case-control study, we tested two athletic populations (i.e. strength athletes, endurance athletes) and a non-athletic, but physically active, control group across two acute exercise bouts, separated by a 2-week period, that measured explosive and high intensity fitness level (repeated 30-s all-out Wingate test (WT)) and cardiorespiratory fitness level (Bruce Treadmill Test). While we did not identify any group differences in alpha and beta diversity or significant differential abundance of microbiome components at baseline, one-third of the species identified were unique to each group. Longitudinal sample (pre- and post-exercise) analysis revealed an abundance of Alistipes communis in the strength group during the WT and 88 species with notable between-group differences during the Bruce Test. SparCC recognized Bifidobacterium longum and Bifidobacterium adolescentis, short-chain fatty acid producers with probiotic properties, species strongly associated with VO2max. Ultimately, we identified several taxa with different baseline abundances and longitudinal changes when comparing individuals based on their VO2max, average power, and maximal power parameters. Our results confirmed that the health status of individuals are consistent with assumptions about microbiome health. Furthermore, our findings indicate that microbiome features are associated with better performance previously identified in elite athletes.
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Affiliation(s)
- Kinga Humińska-Lisowska
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Kinga Zielińska
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow, Poland
| | - Jan Mieszkowski
- Faculty of Health Sciences, University of Lomza, Lomza, Poland
| | | | - Paweł Cięszczyk
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Paweł P Łabaj
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow, Poland
| | - Bartosz Wasąg
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Barbara Frączek
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
- Department of Sports Medicine and Human Nutrition, Institute of Biomedical Sciences, University School of Physical Education, Cracow, Poland
| | - Anna Grzywacz
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | | | - Tomasz Kosciolek
- Malopolska Centre of Biotechnology, Jagiellonian University, Cracow, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
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40
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Yunusbaeva M, Borodina L, Terentyeva D, Bogdanova A, Zakirova A, Bulatov S, Altinbaev R, Bilalov F, Yunusbayev B. Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients. Front Cell Infect Microbiol 2024; 14:1331521. [PMID: 38440790 PMCID: PMC10910113 DOI: 10.3389/fcimb.2024.1331521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction The link between gut microbiota and host immunity motivated numerous studies of the gut microbiome in tuberculosis (TB) patients. However, these studies did not explore the metabolic capacity of the gut community, which is a key axis of impact on the host's immunity. Methods We used deep sequencing of fecal samples from 23 treatment-naive TB patients and 48 healthy donors to reconstruct the gut microbiome's metabolic capacity and strain/species-level content. Results We show that the systematic depletion of the commensal flora of the large intestine, Bacteroidetes, and an increase in Actinobacteria, Firmicutes, and Proteobacteria such as Streptococcaceae, Erysipelotrichaceae, Lachnospiraceae, and Enterobacteriaceae explains the strong taxonomic divergence of the gut community in TB patients. The cumulative expansion of diverse disease-associated pathobionts in patients reached 1/4 of the total gut microbiota, suggesting a heavy toll on host immunity along with MTB infection. Reconstruction of metabolic pathways showed that the microbial community in patients shifted toward rapid growth using glycolysis and excess fermentation to produce acetate and lactate. Higher glucose availability in the intestine likely drives fermentation to lactate and growth, causing acidosis and endotoxemia. Discussion Excessive fermentation and lactic acidosis likely characterize TB patients' disturbed gut microbiomes. Since lactic acidosis strongly suppresses the normal gut flora, directly interferes with macrophage function, and is linked to mortality in TB patients, our findings highlight gut lactate acidosis as a novel research focus. If confirmed, gut acidosis may be a novel potential host-directed treatment target to augment traditional TB treatment.
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Affiliation(s)
- Milyausha Yunusbaeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Liliya Borodina
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Darya Terentyeva
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, Saint Petersburg Pasteur Institute, Saint Petersburg, Russia
| | - Anna Bogdanova
- Laboratory of Evolutionary Biomedicine, International Institute “Solution Chemistry of Advanced Materials and Technologies”, ITMO University, Saint Petersburg, Russia
| | - Aigul Zakirova
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Shamil Bulatov
- Department of Tuberculosis Monitoring, Republican Clinical Antituberculous Dispensary, Ufa, Russia
| | - Radick Altinbaev
- Laboratory of Neurophysiology of Learning, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia
| | - Fanil Bilalov
- Laboratory of Molecular Genetics, Republic Medical Genetic Centre, Ufa, Russia
- Department of Public Health and Health Organization with a course of ICPE, Bashkir State Medical University, Ufa, Russia
| | - Bayazit Yunusbayev
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
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Ross FC, Mayer DE, Gupta A, Gill CIR, Del Rio D, Cryan JF, Lavelle A, Ross RP, Stanton C, Mayer EA. Existing and Future Strategies to Manipulate the Gut Microbiota With Diet as a Potential Adjuvant Treatment for Psychiatric Disorders. Biol Psychiatry 2024; 95:348-360. [PMID: 37918459 DOI: 10.1016/j.biopsych.2023.10.018] [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: 04/11/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 11/04/2023]
Abstract
Nutrition and diet quality play key roles in preventing and slowing cognitive decline and have been linked to multiple brain disorders. This review compiles available evidence from preclinical studies and clinical trials on the impact of nutrition and interventions regarding major psychiatric conditions and some neurological disorders. We emphasize the potential role of diet-related microbiome alterations in these effects and highlight commonalities between various brain disorders related to the microbiome. Despite numerous studies shedding light on these findings, there are still gaps in our understanding due to the limited availability of definitive human trial data firmly establishing a causal link between a specific diet and microbially mediated brain functions and symptoms. The positive impact of certain diets on the microbiome and cognitive function is frequently ascribed with the anti-inflammatory effects of certain microbial metabolites or a reduction of proinflammatory microbial products. We also critically review recent research on pro- and prebiotics and nondietary interventions, particularly fecal microbiota transplantation. The recent focus on diet in relation to brain disorders could lead to improved treatment outcomes with combined dietary, pharmacological, and behavioral interventions.
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Affiliation(s)
- Fiona C Ross
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Dylan E Mayer
- Institute of Human Nutrition, Columbia University, New York, New York
| | - Arpana Gupta
- Goodman-Luskin Microbiome Center, G. Oppenheimer Center for Neurobiology of Stress and Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Chris I R Gill
- Nutrition Innovation Centre for Food and Health, Ulster University, Coleraine, United Kingdom
| | - Daniele Del Rio
- Department of Food and Drugs, University of Parma, Parma, Italy
| | - John F Cryan
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Aonghus Lavelle
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Moorepark Food Research Centre, Fermoy, Cork, Ireland.
| | - Emeran A Mayer
- Goodman-Luskin Microbiome Center, G. Oppenheimer Center for Neurobiology of Stress and Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.
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Cosier DJ, Lambert K, Neale EP, Probst Y, Charlton K. The effect of oral synbiotics on the gut microbiota and inflammatory biomarkers in healthy adults: a systematic review and meta-analysis. Nutr Rev 2024:nuae002. [PMID: 38341803 DOI: 10.1093/nutrit/nuae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024] Open
Abstract
CONTEXT Prior research has explored the effect of synbiotics, the combination of probiotics and prebiotics, on the gut microbiota in clinical populations. However, evidence related to the effect of synbiotics on the gut microbiota in healthy adults has not been reviewed to date. OBJECTIVE A systematic review and meta-analysis was conducted to comprehensively investigate the effect of synbiotics on the gut microbiota and inflammatory markers in populations of healthy adults. DATA SOURCES Scopus, PubMed, Web of Science, ScienceDirect, MEDLINE, CINAHL, and The Cochrane Library were systematically searched to retrieve randomized controlled trials examining the primary outcome of gut microbiota or intestinal permeability changes after synbiotic consumption in healthy adults. Secondary outcomes of interest were short-chain fatty acids, inflammatory biomarkers, and gut microbiota diversity. DATA EXTRACTION Weighted (WMD) or standardized mean difference (SMD) outcome data were pooled in restricted maximum likelihood models using random effects. Twenty-seven articles reporting on 26 studies met the eligibility criteria (n = 1319). DATA ANALYSIS Meta-analyses of 16 studies showed synbiotics resulted in a significant increase in Lactobacillus cell count (SMD, 0.74; 95% confidence interval [CI], 0.15, 1.33; P = 0.01) and propionate concentration (SMD, 0.22; 95% CI, 0.02, 0.43; P = 0.03) compared with controls. A trend for an increase in Bifidobacterium relative abundance (WMD, 0.97; 95% CI, 0.42, 2.52; P = 0.10) and cell count (SMD, 0.82; 95% CI, 0.13, 1.88; P = 0.06) was seen. No significant differences in α-diversity, acetate, butyrate, zonulin, IL-6, CRP, or endotoxins were observed. CONCLUSION This review demonstrates that synbiotics modulate the gut microbiota by increasing Lactobacillus and propionate across various healthy adult populations, and may result in increased Bifidobacterium. Significant variations in synbiotic type, dose, and duration should be considered as limitations when applying findings to clinical practice. SYSTEMATIC REVIEW REGISTRATION PROSPERO no. CRD42021284033.
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Affiliation(s)
- Denelle J Cosier
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kelly Lambert
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Elizabeth P Neale
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Yasmine Probst
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Karen Charlton
- School of Medicine, Indigenous and Health Sciences, University of Wollongong, Wollongong, New South Wales, Australia
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Vestergaard MV, Allin KH, Eriksen C, Zakerska-Banaszak O, Arasaradnam RP, Alam MT, Kristiansen K, Brix S, Jess T. Gut microbiota signatures in inflammatory bowel disease. United European Gastroenterol J 2024; 12:22-33. [PMID: 38041519 PMCID: PMC10859715 DOI: 10.1002/ueg2.12485] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/10/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence. OBJECTIVES Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients. METHODS We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms. RESULTS Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found. CONCLUSIONS Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.
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Affiliation(s)
- Marie Vibeke Vestergaard
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
| | - Kristine H Allin
- 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
| | - Carsten Eriksen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Ramesh P Arasaradnam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
| | - Mohammad T Alam
- Warwick Medical School & Cancer Research Centre, University of Leicester, Leicester, UK
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Karsten Kristiansen
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Brix
- Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - 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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44
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Heiskanen MA, Aatsinki A, Hakonen P, Kartiosuo N, Munukka E, Lahti L, Keskitalo A, Huovinen P, Niinikoski H, Viikari J, Rönnemaa T, Lagström H, Jula A, Raitakari O, Rovio SP, Pahkala K. Association of Long-Term Habitual Dietary Fiber Intake since Infancy with Gut Microbiota Composition in Young Adulthood. J Nutr 2024; 154:744-754. [PMID: 38219864 DOI: 10.1016/j.tjnut.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Dietary fiber is an important health-promoting component of the diet, which is fermented by the gut microbes that produce metabolites beneficial for the host's health. OBJECTIVES We studied the associations of habitual long-term fiber intake from infancy with gut microbiota composition in young adulthood by leveraging data from the Special Turku Coronary Risk Factor Intervention Project, an infancy-onset 20-y dietary counseling study. METHODS Fiber intake was assessed annually using food diaries from infancy ≤ age 20 y. At age 26 y, the first postintervention follow-up study was conducted including food diaries and fecal sample collection (N = 357). Cumulative dietary fiber intake was assessed as the area under the curve for energy-adjusted fiber intake throughout the study (age 0-26 y). Gut microbiota was profiled using 16S ribosomal ribonucleic acid amplicon sequencing. The primary outcomes were 1) α diversity expressed as the observed richness and Shannon index, 2) β diversity using Bray-Curtis dissimilarity scores, and 3) differential abundance of each microbial taxa with respect to the cumulative energy-adjusted dietary fiber intake. RESULTS Higher cumulative dietary fiber intake was associated with decreased Shannon index (β = -0.019 per unit change in cumulative fiber intake, P = 0.008). Overall microbial community composition was related to the amount of fiber consumed (permutational analysis of variation R2 = 0.005, P = 0.024). The only genus that was increased with higher cumulative fiber intake was butyrate-producing Butyrivibrio (log2 fold-change per unit change in cumulative fiber intake 0.40, adjusted P = 0.023), whereas some other known butyrate producers such as Faecalibacterium and Subdoligranulum were decreased with higher cumulative fiber intake. CONCLUSIONS As early-life nutritional exposures may affect the lifetime microbiota composition and disease risk, this study adds novel information on the associations of long-term dietary fiber intake with the gut microbiota. This trial was registered at clinicaltrials.gov as NCT00223600.
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Affiliation(s)
- Marja A Heiskanen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.
| | - Anna Aatsinki
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Petra Hakonen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Noora Kartiosuo
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Eveliina Munukka
- Turku Clinical Microbiome Biobank, Department of Clinical Microbiology, Turku University Hospital, Turku, Finland; Institute of Biomedicine, University of Turku, Turku, Finland
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
| | - Anniina Keskitalo
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Pentti Huovinen
- Institute of Biomedicine, University of Turku, Turku, Finland; Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Harri Niinikoski
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Pediatrics, University of Turku, Turku, Finland
| | - Jorma Viikari
- Department of Medicine, University of Turku, Turku, Finland; Division of Medicine, Turku University Hospital, Turku, Finland
| | - Tapani Rönnemaa
- Department of Medicine, University of Turku, Turku, Finland; Division of Medicine, Turku University Hospital, Turku, Finland
| | - Hanna Lagström
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Public Health, Turku University Hospital, University of Turku, Turku, Finland
| | - Antti Jula
- Department of Public Health Solutions, Institute for Health and Welfare, Turku, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Suvi P Rovio
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Public Health, Turku University Hospital, University of Turku, Turku, Finland
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Paavo Nurmi Centre and Unit for Health and Physical Activity, University of Turku, Turku, Finland
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45
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Godny L, Dotan I. Is the Mediterranean Diet in Inflammatory Bowel Diseases Ready for Prime Time? J Can Assoc Gastroenterol 2024; 7:97-103. [PMID: 38314171 PMCID: PMC10836973 DOI: 10.1093/jcag/gwad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2024] Open
Abstract
Background The rising incidence of inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), specifically in the developing world, suggests an important environmental effect. Amongst environmental influences, dietary factors, particularly the adoption of a westernized diet, have been specifically noticed. In contrast, the Mediterranean diet (MED), characterized by high intake of fruits, vegetables, whole grains, legumes, nuts, olive oil, and moderate consumption of animal and ultra processed foods, has shown potential positive effects in IBD. Methods Here we conducted a narrative review focusing on the evidence regarding the role of MED in IBD prevention and management. Results Epidemiological studies suggest inverse association of MED with CD development. Furthermore, adherence to MED has been associated with clinical improvement in active CD and maintenance of lower levels of inflammatory markers in UC, along with improved quality of life and lower mortality rates in IBD patients. Mechanistically, MED promotes a diverse and beneficial gut microbiota, possesses anti-inflammatory properties through polyphenols and dietary fats, and may modulate oxidative stress. In clinical practice, MED may be adapted to diverse disease phenotypes and cultural preferences, and is a sustainable, easy to maintain dietary approach. Conclusion Current evidence may support the integration of MED into clinical practice in IBD care. In future research, the efficacy of MED in specific IBD phenotypes should be assessed.
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Affiliation(s)
- Lihi Godny
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, 49100, Israel
- Nutrition Unit, Rabin Medical Center, Petah-Tikva, 49100, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, 49100, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
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Wallin N, Bergman L, Smith GN. Pregnancy-associated cardiovascular risks and postpartum care; an opportunity for interventions aiming at health preservation and disease prevention. Best Pract Res Clin Obstet Gynaecol 2024; 92:102435. [PMID: 38048671 DOI: 10.1016/j.bpobgyn.2023.102435] [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: 04/26/2023] [Revised: 07/20/2023] [Accepted: 11/18/2023] [Indexed: 12/06/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of premature death and disability for female individuals around the world and the rates are increasing in those aged 35-44 years. Certain pregnancy complications (Pregnancy-associated Cardiovascular Risks (P-CVR))are linked to an increased risk of future CVD making pregnancy and the postpartum period as an ideal time to screen individuals for underlying, often unrecognized, cardiovascular risk factors. Pregnancy complications associated with an increased risk of future CVD including the hypertensive disorders of pregnancy, gestational diabetes, idiopathic preterm birth, delivery of a growth restricted baby and a placental abruption that leads to delivery. A number of guidelines and research groups recommend postpartum CVR screening, counseling and lifestyle intervention for all those who have had one or more of P-CVRs starting within the first six months postpartum. An individualized plan for postpartum screening should be created with the individual and lifestyle interventions discussed.
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Affiliation(s)
- Nicole Wallin
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lina Bergman
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Stellenbosch University, Cape Town, South Africa; Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Graeme N Smith
- Department of Obstetrics and Gynecology, Queen's University, Ontario, Canada.
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Wang Q, Fan X, Wu S, Su X. PM-CNN: microbiome status recognition and disease detection model based on phylogeny and multi-path neural network. BIOINFORMATICS ADVANCES 2024; 4:vbae013. [PMID: 38371919 PMCID: PMC10873578 DOI: 10.1093/bioadv/vbae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
Motivation The human microbiome, found throughout various body parts, plays a crucial role in health dynamics and disease development. Recent research has highlighted microbiome disparities between patients with different diseases and healthy individuals, suggesting the microbiome's potential in recognizing health states. Traditionally, microbiome-based status classification relies on pre-trained machine learning (ML) models. However, most ML methods overlook microbial relationships, limiting model performance. Results To address this gap, we propose PM-CNN (Phylogenetic Multi-path Convolutional Neural Network), a novel phylogeny-based neural network model for multi-status classification and disease detection using microbiome data. PM-CNN organizes microbes based on their phylogenetic relationships and extracts features using a multi-path convolutional neural network. An ensemble learning method then fuses these features to make accurate classification decisions. We applied PM-CNN to human microbiome data for status and disease detection, demonstrating its significant superiority over existing ML models. These results provide a robust foundation for microbiome-based state recognition and disease prediction in future research and applications. Availability and implementation PM-CNN software is available at https://github.com/qdu-bioinfo/PM_CNN.
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Affiliation(s)
- Qiangqiang Wang
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China
| | - Xiaoqian Fan
- Department of Gastroenterology, Shouguang Hospital of Traditional Chinese Medicine, Weifang 262700, China
| | - Shunyao Wu
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University, Qingdao 266071, China
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Gul F, Herrema H, Davids M, Keating C, Nasir A, Ijaz UZ, Javed S. Gut microbial ecology and exposome of a healthy Pakistani cohort. Gut Pathog 2024; 16:5. [PMID: 38254227 PMCID: PMC10801943 DOI: 10.1186/s13099-024-00596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Pakistan is a multi-ethnic society where there is a disparity between dietary habits, genetic composition, and environmental exposures. The microbial ecology of healthy Pakistani gut in the context of anthropometric, sociodemographic, and dietary patterns holds interest by virtue of it being one of the most populous countries, and also being a Lower Middle Income Country (LMIC). METHODS 16S rRNA profiling of healthy gut microbiome of normo-weight healthy Pakistani individuals from different regions of residence is performed with additional meta-data collected through filled questionnaires. The current health status is then linked to dietary patterns through [Formula: see text] test of independence and Generalized Linear Latent Variable Model (GLLVM) where distribution of individual microbes is regressed against all recorded sources of variability. To identify the core microbiome signature, a dynamic approach is used that considers into account species occupancy as well as consistency across assumed grouping of samples including organization by gender and province of residence. Fitting neutral modeling then revealed core microbiome that is selected by the environment. RESULTS A strong determinant of disparity is by province of residence. It is also established that the male microbiome is better adapted to the local niche than the female microbiome, and that there is microbial taxonomic and functional diversity in different ethnicities, dietary patterns and lifestyle habits. Some microbial genera, such as, Megamonas, Porphyromonas, Haemophilus, Klebsiella and Finegoldia showed significant associations with consumption of pickle, fresh fruits, rice, and cheese. Our analyses suggest current health status being associated with the diet, sleeping patterns, employment status, and the medical history. CONCLUSIONS This study provides a snapshot of the healthy core Pakistani gut microbiome by focusing on the most populous provinces and ethnic groups residing in predominantly urban areas. The study serves a reference dataset for exploring variations in disease status and designing personalized dietary and lifestyle interventions to promote gut health, particularly in LMICs settings.
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Affiliation(s)
- Farzana Gul
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Mark Davids
- Department of Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Ciara Keating
- School of Biodiversity, One Health & Veterinary Medicine, Graham Kerr Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Arshan Nasir
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan
- Moderna, Inc., Cambridge, MA, USA
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, G11 6EW, UK.
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, L69 7BE, UK.
- National University of Ireland, Galway, University Road, Galway, H91 TK33, Ireland.
| | - Sundus Javed
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 45550, Pakistan.
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Wu Q, Badu S, So SY, Treangen TJ, Savidge TC. The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease. J Clin Invest 2024; 134:e170859. [PMID: 37962956 PMCID: PMC10786686 DOI: 10.1172/jci170859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Targeted metagenomic sequencing is an emerging strategy to survey disease-specific microbiome biomarkers for clinical diagnosis and prognosis. However, this approach often yields inconsistent or conflicting results owing to inadequate study power and sequencing bias. We introduce Taxa4Meta, a bioinformatics pipeline explicitly designed to compensate for technical and demographic bias. We designed and validated Taxa4Meta for accurate taxonomic profiling of 16S rRNA amplicon data acquired from different sequencing strategies. Taxa4Meta offers significant potential in identifying clinical dysbiotic features that can reliably predict human disease, validated comprehensively via reanalysis of individual patient 16S data sets. We leveraged the power of Taxa4Meta's pan-microbiome profiling to generate 16S-based classifiers that exhibited excellent utility for stratification of diarrheal patients with Clostridioides difficile infection, irritable bowel syndrome, or inflammatory bowel diseases, which represent common misdiagnoses and pose significant challenges for clinical management. We believe that Taxa4Meta represents a new "best practices" approach to individual microbiome surveys that can be used to define gut dysbiosis at a population-scale level.
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Affiliation(s)
- Qinglong Wu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Shyam Badu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Sik Yu So
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Tor C. Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
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Jarma D, Maestre JP, Sanchez J, Brodfuehrer S, Katz LE, Horner S, Kinney KA. Participant-collected household dust for assessing microorganisms and semi-volatile organic compounds in urban homes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168230. [PMID: 37951260 DOI: 10.1016/j.scitotenv.2023.168230] [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: 08/09/2023] [Revised: 10/17/2023] [Accepted: 10/28/2023] [Indexed: 11/13/2023]
Abstract
Dust samples collected by researchers and study participants from 43 U.S. urban homes were analyzed and compared to evaluate the feasibility of using participant-collected samples to assess indoor environmental exposures. The microbial and chemical composition of participant-collected (and shipped) samples were compared to researcher-collected samples from the same household, using dust recovered from each home's heating, ventilation, and air conditioning (HVAC) filter. The bacterial and fungal communities present in all dust samples were determined via MiSeq 16S and ITS sequencing, and the concentrations of 27 semi-volatile organic compounds (7 orthophosphates, 6 phthalates, and 14 brominated flame retardants) were determined via GC-MS. Self-report data on the home environment was collected via an online survey of study participants. While the researcher-collected samples (RCS) yielded greater mass than the participant-collected samples (PCS), the alpha and beta diversities of the bacterial and fungal communities recovered in the RCS and PCS were not significantly different, indicating that PCS is a viable option for indoor microbiome studies of residential homes. The microbial communities recovered in both cases reflected the dominance of human-associated bacterial taxa and outdoor-associated fungal taxa with similar pathogen-associated taxa present in each sample type. In both PCS and RCS, the amount of carpet in the home and the frequency of bleach use had a significant effect on the composition of fungal communities. Semi-volatile organic compounds (SVOCs) of potential human health concern, were commonly detected in the homes. Organophosphates and phthalates were recovered at a similar frequency in both PCS and RCS. Measured SVOC concentration levels were consistent with previous indoor studies although differences were observed between PCS and RCS for several SVOCs. This study demonstrates the potential and challenges associated with participant-collected dust samples for indoor environment studies.
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Affiliation(s)
- D Jarma
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, TX, USA
| | - J P Maestre
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, TX, USA
| | - J Sanchez
- School of Social Work, The University of Texas at Austin, TX, USA
| | - S Brodfuehrer
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, TX, USA
| | - L E Katz
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, TX, USA
| | - S Horner
- School of Nursing, The University of Texas at Austin, TX, USA
| | - K A Kinney
- Department of Civil, Architectural, and Environmental Engineering, The University of Texas at Austin, TX, USA.
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