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McKee K, Bassis CM, Golob J, Palazzolo B, Sen A, Comstock SS, Rosas-Salazar C, Stanford JB, O'Connor T, Gern JE, Paneth N, Dunlop AL. Host factors are associated with vaginal microbiome structure in pregnancy in the ECHO Cohort Consortium. Sci Rep 2024; 14:11798. [PMID: 38782975 PMCID: PMC11116393 DOI: 10.1038/s41598-024-62537-7] [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: 11/09/2023] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
Using pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental influences on Child Health Outcomes (ECHO) Program, we analyzed 16S rRNA gene amplicon sequences to identify clinical and demographic host factors that associate with vaginal microbiota structure in pregnancy both within and across diverse cohorts. Using PERMANOVA models, we assessed factors associated with vaginal community structure in pregnancy, examined whether host factors were conserved across populations, and tested the independent and combined effects of host factors on vaginal community state types (CSTs) using multinomial logistic regression models. Demographic and social factors explained a larger amount of variation in the vaginal microbiome in pregnancy than clinical factors. After adjustment, lower education, rather than self-identified race, remained a robust predictor of L. iners dominant (CST III) and diverse (CST IV) (OR = 8.44, 95% CI = 4.06-17.6 and OR = 4.18, 95% CI = 1.88-9.26, respectively). In random forest models, we identified specific taxonomic features of host factors, particularly urogenital pathogens associated with pregnancy complications (Aerococcus christensenii and Gardnerella spp.) among other facultative anaerobes and key markers of community instability (L. iners). Sociodemographic factors were robustly associated with vaginal microbiota structure in pregnancy and should be considered as sources of variation in human microbiome studies.
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Grants
- U24OD023382 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- U2C OD023375 NIH HHS
- UH3 OD023271 NIH HHS
- UH3 OD023282 NIH HHS
- UH3OD023282 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- UH3 OD023287 NIH HHS
- U24 OD023319 NIH HHS
- UH3 OD023305 NIH HHS
- K01 AI153558 NIAID NIH HHS
- UH3 OD023288 NIH HHS
- UH3OD023249 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- U24OD023319 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- UH3 OD023349 NIH HHS
- UH3 OD023337 NIH HHS
- UH3 OD023328 NIH HHS
- U24 OD023382 NIH HHS
- UH3 OD023313 NIH HHS
- UH3 OD023289 NIH HHS
- UH3 OD023249 NIH HHS
- UH3 OD023389 NIH HHS
- UH3 OD023290 NIH HHS
- UH3OD023251 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- UH3 OD023285 NIH HHS
- UH3 OD023275 NIH HHS
- UH3 OD023318 NIH HHS
- UH3 OD023248 NIH HHS
- U2COD023375 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- UH3 OD023253 NIH HHS
- UH3 OD023272 NIH HHS
- UH3 OD023347 NIH HHS
- UH3OD023318 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- UH3 OD023251 NIH HHS
- UH3 OD023279 NIH HHS
- UH3OD023285 Environmental influences on Child Health Outcomes (ECHO) program, Office of the Director, National Institutes of Health
- UH3 OD023244 NIH HHS
- UH3 OD023320 NIH HHS
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Affiliation(s)
- Kimberly McKee
- Department of Family Medicine, University of Michigan, 1018 Fuller St, Ann Arbor, MI, 48104, USA.
| | - Christine M Bassis
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Beatrice Palazzolo
- Department of Family Medicine, University of Michigan, 1018 Fuller St, Ann Arbor, MI, 48104, USA
| | - Ananda Sen
- Department of Family Medicine, University of Michigan, 1018 Fuller St, Ann Arbor, MI, 48104, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, USA
| | | | - Joseph B Stanford
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Thomas O'Connor
- Departments of Neuroscience and Obstetrics & Gynecology, University of Rochester, Rochester, NY, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | - Nigel Paneth
- Departments of Epidemiology & Biostatistics and Pediatrics & Human Development, Michigan State University, East Lansing, MI, USA
| | - Anne L Dunlop
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
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Yonatan Y, Kahn S, Bashan A. Interactions-based classification of a single microbial sample. CELL REPORTS METHODS 2024; 4:100775. [PMID: 38744286 PMCID: PMC11133833 DOI: 10.1016/j.crmeth.2024.100775] [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: 06/14/2023] [Revised: 02/11/2024] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
To address the limitation of overlooking crucial ecological interactions due to relying on single time point samples, we developed a computational approach that analyzes individual samples based on the interspecific microbial relationships. We verify, using both numerical simulations as well as real and shuffled microbial profiles from the human oral cavity, that the method can classify single samples based on their interspecific interactions. By analyzing the gut microbiome of people with autistic spectrum disorder, we found that our interaction-based method can improve the classification of individual subjects based on a single microbial sample. These results demonstrate that the underlying ecological interactions can be practically utilized to facilitate microbiome-based diagnosis and precision medicine.
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Affiliation(s)
- Yogev Yonatan
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel
| | - Shaya Kahn
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel
| | - Amir Bashan
- Physics Department, Bar-Ilan University, Ramat-Gan, Israel.
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3
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Warren A, Nyavor Y, Zarabian N, Mahoney A, Frame LA. The microbiota-gut-brain-immune interface in the pathogenesis of neuroinflammatory diseases: a narrative review of the emerging literature. Front Immunol 2024; 15:1365673. [PMID: 38817603 PMCID: PMC11137262 DOI: 10.3389/fimmu.2024.1365673] [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: 01/04/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Importance Research is beginning to elucidate the sophisticated mechanisms underlying the microbiota-gut-brain-immune interface, moving from primarily animal models to human studies. Findings support the dynamic relationships between the gut microbiota as an ecosystem (microbiome) within an ecosystem (host) and its intersection with the host immune and nervous systems. Adding this to the effects on epigenetic regulation of gene expression further complicates and strengthens the response. At the heart is inflammation, which manifests in a variety of pathologies including neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Multiple Sclerosis (MS). Observations Generally, the research to date is limited and has focused on bacteria, likely due to the simplicity and cost-effectiveness of 16s rRNA sequencing, despite its lower resolution and inability to determine functional ability/alterations. However, this omits all other microbiota including fungi, viruses, and phages, which are emerging as key members of the human microbiome. Much of the research has been done in pre-clinical models and/or in small human studies in more developed parts of the world. The relationships observed are promising but cannot be considered reliable or generalizable at this time. Specifically, causal relationships cannot be determined currently. More research has been done in Alzheimer's disease, followed by Parkinson's disease, and then little in MS. The data for MS is encouraging despite this. Conclusions and relevance While the research is still nascent, the microbiota-gut-brain-immune interface may be a missing link, which has hampered our progress on understanding, let alone preventing, managing, or putting into remission neurodegenerative diseases. Relationships must first be established in humans, as animal models have been shown to poorly translate to complex human physiology and environments, especially when investigating the human gut microbiome and its relationships where animal models are often overly simplistic. Only then can robust research be conducted in humans and using mechanistic model systems.
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Affiliation(s)
- Alison Warren
- The Frame-Corr Laboratory, Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Yvonne Nyavor
- Department of Biotechnology, Harrisburg University of Science and Technology, Harrisburg, PA, United States
| | - Nikkia Zarabian
- The Frame-Corr Laboratory, Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Aidan Mahoney
- The Frame-Corr Laboratory, Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- Undergraduate College, Princeton University, Princeton, NJ, United States
| | - Leigh A. Frame
- The Frame-Corr Laboratory, Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
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4
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Huangfu W, Cao S, Li S, Zhang S, Liu M, Liu B, Zhu X, Cui Y, Wang Z, Zhao J, Shi Y. In vitro and in vivo fermentation models to study the function of dietary fiber in pig nutrition. Appl Microbiol Biotechnol 2024; 108:314. [PMID: 38683435 PMCID: PMC11058960 DOI: 10.1007/s00253-024-13148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
The importance of dietary fiber (DF) in animal diets is increasing with the advancement of nutritional research. DF is fermented by gut microbiota to produce metabolites, which are important in improving intestinal health. This review is a systematic review of DF in pig nutrition using in vitro and in vivo models. The fermentation characteristics of DF and the metabolic mechanisms of its metabolites were summarized in an in vitro model, and it was pointed out that SCFAs and gases are the important metabolites connecting DF, gut microbiota, and intestinal health, and they play a key role in intestinal health. At the same time, some information about host-microbe interactions could have been improved through traditional animal in vivo models, and the most direct feedback on nutrients was generated, confirming the beneficial effects of DF on sow reproductive performance, piglet intestinal health, and growing pork quality. Finally, the advantages and disadvantages of different fermentation models were compared. In future studies, it is necessary to flexibly combine in vivo and in vitro fermentation models to profoundly investigate the mechanism of DF on the organism in order to promote the development of precision nutrition tools and to provide a scientific basis for the in-depth and rational utilization of DF in animal husbandry. KEY POINTS: • The fermentation characteristics of dietary fiber in vitro models were reviewed. • Metabolic pathways of metabolites and their roles in the intestine were reviewed. • The role of dietary fiber in pigs at different stages was reviewed.
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Affiliation(s)
- Weikang Huangfu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
| | - Shixi Cao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
| | - Shouren Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
| | - Shuhang Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
| | - Mengqi Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
| | - Boshuai Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Forage Engineering Technology Research Center, Zhengzhou, 450002, Henan, China
| | - Xiaoyan Zhu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Forage Engineering Technology Research Center, Zhengzhou, 450002, Henan, China
| | - Yalei Cui
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Forage Engineering Technology Research Center, Zhengzhou, 450002, Henan, China
| | - Zhichang Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China
- Henan Forage Engineering Technology Research Center, Zhengzhou, 450002, Henan, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, USA
| | - Yinghua Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, No.15 Longzihu University Area, Zhengdong New District, Zhengzhou, 450046, China.
- Henan Key Laboratory of Innovation and Utilization of Grassland Resources, Zhengzhou, China.
- Henan Forage Engineering Technology Research Center, Zhengzhou, 450002, Henan, China.
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5
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Ouyang Q, Li X, Liang Y, Liu R. Sea Buckthorn Polysaccharide Ameliorates Colitis. Nutrients 2024; 16:1280. [PMID: 38732527 PMCID: PMC11085905 DOI: 10.3390/nu16091280] [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: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 05/13/2024] Open
Abstract
Ulcerative colitis (UC) is characterized by chronic inflammation and ulceration of the intestinal inner lining, resulting in various symptoms. Sea buckthorn berries contain a bioactive compound known as sea buckthorn polysaccharide (SBP). However, the precise mechanisms underlying the impact of SBP on UC remain unclear. In this study, we investigated the effects of pretreatment with SBP on colitis induced by DSS. Our findings demonstrate that SBP pretreatment effectively reduces inflammation, oxidative stress, and intestinal barrier damage associated with colitis. To further elucidate the role of SBP-modulated gut microbiota in UC, we performed fecal microbiota transplantation (FMT) on DSS-treated mice. The microbiota from SBP-treated mice exhibits notable anti-inflammatory and antioxidant effects, improves colonic barrier integrity, and increases the abundance of beneficial bacteria, as well as enhancing SCFA production. Collectively, these results strongly indicate that SBP-mediated amelioration of colitis is attributed to its impact on the gut microbiota, particularly through the promotion of SCFA-producing bacteria and subsequent elevation of SCFA levels. This study provides compelling evidence supporting the efficacy of pre-emptive SBP supplementation in alleviating colitis symptoms by modulating the gut microbiota, thereby offering novel insights into the potential of SBP as a regulator of the gut microbiota for colitis relief.
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Affiliation(s)
- Qinqin Ouyang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210000, China; (Q.O.)
| | - Xin Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210000, China
| | - Yongheng Liang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210000, China; (Q.O.)
| | - Rong Liu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210000, China
- Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
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6
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Pinnell LJ, Wolfe CA, Castle J, Crosby WB, Doster E, Morley PS. Effectiveness of stabilization methods for the immediate and short-term preservation of bovine fecal and upper respiratory tract genomic DNA. PLoS One 2024; 19:e0300285. [PMID: 38564604 PMCID: PMC10987004 DOI: 10.1371/journal.pone.0300285] [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: 11/22/2023] [Accepted: 02/24/2024] [Indexed: 04/04/2024] Open
Abstract
Previous research on stabilization methods for microbiome investigations has largely focused on human fecal samples. There are a few studies using feces from other species, but no published studies investigating preservation of samples collected from cattle. Given that microbial taxa are differentially impacted during storage it is warranted to study impacts of preservation methods on microbial communities found in samples outside of human fecal samples. Here we tested methods of preserving bovine fecal respiratory specimens for up to 2 weeks at four temperatures (room temperature, 4°C, -20°C, and -80°C) by comparing microbial diversity and community composition to samples extracted immediately after collection. Importantly, fecal specimens preserved and analyzed were technical replicates, providing a look at the effects of preservation method in the absence of biological variation. We found that preservation with the OMNIgene®•GUT kit resulted in community structure most like that of fresh samples extracted immediately, even when stored at room temperature (~20°C). Samples that were flash-frozen without added preservation solution were the next most representative of original communities, while samples preserved with ethanol were the least representative. These results contradict previous reports that ethanol is effective in preserving fecal communities and suggest for studies investigating cattle either flash-freezing of samples without preservative or preservation with OMNIgene®•GUT will yield more representative microbial communities.
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Affiliation(s)
- Lee J. Pinnell
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - Cory A. Wolfe
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - Jake Castle
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - William B. Crosby
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi State, United States of America
| | - Enrique Doster
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - Paul S. Morley
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
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7
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Tsuruga T, Fujimoto H, Yasuma T, D'Alessandro-Gabazza CN, Toda M, Ito T, Tomaru A, Saiki H, Okano T, Alhawsawi MAB, Takeshita A, Nishihama K, Takei R, Kondoh Y, Cann I, Gabazza EC, Kobayashi T. Role of microbiota-derived corisin in coagulation activation during SARS-CoV-2 infection. J Thromb Haemost 2024:S1538-7836(24)00118-1. [PMID: 38453025 DOI: 10.1016/j.jtha.2024.02.014] [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: 09/27/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Coagulopathy is a major cause of morbidity and mortality in COVID-19 patients. Hypercoagulability in COVID-19 results in deep vein thrombosis, thromboembolic complications, and diffuse intravascular coagulation. Microbiome dysbiosis influences the clinical course of COVID-19. However, the role of dysbiosis in COVID-19-associated coagulopathy is not fully understood. OBJECTIVES The present study tested the hypothesis that the microbiota-derived proapoptotic corisin is involved in the coagulation system activation during SARS-CoV-2 infection. METHODS This cross-sectional study included 47 consecutive patients who consulted for symptoms of COVID-19. A mouse acute lung injury model was used to recapitulate the clinical findings. A549 alveolar epithelial, THP-1, and human umbilical vein endothelial cells were used to evaluate procoagulant and anticoagulant activity of corisin. RESULTS COVID-19 patients showed significantly high circulating levels of corisin, thrombin-antithrombin complex, D-dimer, tumor necrosis factor-α, and monocyte-chemoattractant protein-1 with reduced levels of free protein S compared with healthy subjects. The levels of thrombin-antithrombin complex, D-dimer, and corisin were significantly correlated. A monoclonal anticorisin-neutralizing antibody significantly inhibited the inflammatory response and coagulation system activation in a SARS-CoV-2 spike protein-associated acute lung injury mouse model, and the levels of corisin and thrombin-antithrombin complex were significantly correlated. In an in vitro experiment, corisin increased the tissue factor activity and decreased the anticoagulant activity of thrombomodulin in epithelial, endothelial, and monocytic cells. CONCLUSION The microbiota-derived corisin is significantly increased and correlated with activation of the coagulation system during SARS-CoV-2 infection, and corisin may directly increase the procoagulant activity in epithelial, endothelial, and monocytic cells.
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Affiliation(s)
- Tatsuki Tsuruga
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Hajime Fujimoto
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Taro Yasuma
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan; Department of Diabetes, Endocrinology and Metabolism, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Corina N D'Alessandro-Gabazza
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Masaaki Toda
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Toshiyuki Ito
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Atsushi Tomaru
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Haruko Saiki
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Tomohito Okano
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Manal A B Alhawsawi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Atsuro Takeshita
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Department of Diabetes, Endocrinology and Metabolism, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Kota Nishihama
- Department of Diabetes, Endocrinology and Metabolism, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Reoto Takei
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, Seto, Aichi, Japan
| | - Yasuhiro Kondoh
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, Seto, Aichi, Japan
| | - Isaac Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Animal Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Esteban C Gabazza
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Tetsu Kobayashi
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan
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8
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Law SR, Mathes F, Paten AM, Alexandre PA, Regmi R, Reid C, Safarchi A, Shaktivesh S, Wang Y, Wilson A, Rice SA, Gupta VVSR. Life at the borderlands: microbiomes of interfaces critical to One Health. FEMS Microbiol Rev 2024; 48:fuae008. [PMID: 38425054 PMCID: PMC10977922 DOI: 10.1093/femsre/fuae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 02/12/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological, evolutionary, and molecular processes governing the establishment and function of microbiome-host relationships, specifically at interfaces critical to One Health-a transdisciplinary framework that recognizes that the health outcomes of people, animals, plants, and the environment are tightly interconnected. Within the context of One Health, the core principles underpinning microbiome assembly will be discussed in detail, including biofilm formation, microbial recruitment strategies, mechanisms of microbial attachment, community succession, and the effect these processes have on host function and health. Finally, this review will catalogue recent advances in microbiology and microbial ecology methods that can be used to profile microbial interfaces, with particular attention to multi-omic, advanced imaging, and modelling approaches. These technologies are essential for delineating the general and specific principles governing microbiome assembly and functions, mapping microbial interconnectivity across varying spatial and temporal scales, and for the establishment of predictive frameworks that will guide the development of targeted microbiome-interventions to deliver One Health outcomes.
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Affiliation(s)
- Simon R Law
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Falko Mathes
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Floreat, WA 6014, Australia
| | - Amy M Paten
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Canberra, ACT 2601, Australia
| | - Pamela A Alexandre
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, St Lucia, Qld 4072, Australia
| | - Roshan Regmi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
| | - Cameron Reid
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Environment, Urrbrae, SA 5064, Australia
| | - Azadeh Safarchi
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Westmead, NSW 2145, Australia
| | - Shaktivesh Shaktivesh
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Data 61, Clayton, Vic 3168, Australia
| | - Yanan Wang
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Adelaide SA 5000, Australia
| | - Annaleise Wilson
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Health and Biosecurity, Geelong, Vic 3220, Australia
| | - Scott A Rice
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture, and Food, Westmead, NSW 2145, Australia
| | - Vadakattu V S R Gupta
- CSIRO MOSH-Future Science Platform, Australia
- CSIRO Agriculture and Food, Urrbrae, SA 5064, Australia
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9
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Longitudinal analysis shows how microbiome changes might influence responses to immune checkpoint blockade. Nat Med 2024; 30:644-645. [PMID: 38388842 DOI: 10.1038/s41591-024-02830-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
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10
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Kang HY, Choe EK. Clinical Strategies in Gene Screening Counseling for the Healthy General Population. Korean J Fam Med 2024; 45:61-68. [PMID: 38528647 DOI: 10.4082/kjfm.23.0254] [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: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 03/27/2024] Open
Abstract
The burgeoning interest in precision medicine has propelled an increase in the use of genome tests for screening purposes within the healthy population. Gene screening tests aim to pre-emptively identify those individuals who may be genetically predisposed to certain diseases. However, as genetic screening becomes more commonplace, it is essential to acknowledge the unique challenges it poses. A prevalent issue in this regard is the occurrence of falsepositive results, which can lead to unnecessary additional tests or treatments, and psychological distress. Additionally, the interpretation of genomic variants is based on current research evidence, and can accordingly change as new research findings emerge, potentially altering the clinical significance of these variants. Conversely, a further prominent concern regards false assurances in genetic testing, as genetic tests can yield false-negative results, potentially posing a significant clinical risk. Moreover, the results obtained for the same disease can vary among different genetic testing services, due to differences in the types of variants assessed, the scope of tests, analytical methods, and the algorithms used for predicting diseases. Consequently, whereas genetic testing holds significant promise for the future of medicine, it poses unique challenges. If conducted without a full understanding of its implications, genetic testing may fail to achieve its purpose potentially hindering effective health management. Therefore, to ensure a comprehensive understanding of the implications of genetic testing within the general population, sufficient discussion and careful consideration should be given to counseling based on gene test results.
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Affiliation(s)
- Hae Yeon Kang
- Department of Internal Medicine, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Eun Kyung Choe
- Department of Surgery, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
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11
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Berg G, Dorador C, Egamberdieva D, Kostka JE, Ryu CM, Wassermann B. Shared governance in the plant holobiont and implications for one health. FEMS Microbiol Ecol 2024; 100:fiae004. [PMID: 38364305 PMCID: PMC10876113 DOI: 10.1093/femsec/fiae004] [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: 09/15/2023] [Revised: 10/30/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Angamos 601, Antofagasta, Chile
| | - Dilfuza Egamberdieva
- Institute of Fundamental and Applied Research, National Research University, TIIAME, Kari Niyazi street 39, Tashkent 100000, Uzbekistan
- Medical School, Central Asian University, Milliy bog street 264, Tashkent 111221, Uzbekistan
| | - Joel E Kostka
- Schools of Biological Sciences and Earth & Atmospheric Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332, United States
| | - Choong-Min Ryu
- Biosystems and Bioengineering, University of Science and Technology KRIBB School, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, 125 Gwahangro, Yuseong, Daejeon 34141, South Korea
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
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12
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Shinkura R. Development of Orally Ingestible IgA Antibody Drugs to Maintain Symbiosis Between Humans and Microorganisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:165-176. [PMID: 38467979 DOI: 10.1007/978-981-99-9781-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
In recent years, dysbiosis, abnormalities in the gut microbiota, has been reported to be associated with the development of many diseases, and improving the gut microbiota is important for health maintenance. It has been shown that the host recognizes and regulates intestinal bacteria by means of IgA antibodies secreted into the gut, but the precise nature of the commensal gut bacteria recognized by each IgA antibody is unclear. We have cloned monoclonal IgA antibodies from mouse intestinal IgA-producing cells and are searching for bacterial molecules recognized by each IgA clone. Although the interaction of IgA antibodies with intestinal bacteria is still largely unknown and requires further basic research, we discuss the potential use of orally ingestible IgA antibodies as agents to improve intestinal microbiota.
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Affiliation(s)
- Reiko Shinkura
- Laboratory of Immunology and Infection Control, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
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13
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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14
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Seppi M, Pasqualini J, Facchin S, Savarino EV, Suweis S. Emergent Functional Organization of Gut Microbiomes in Health and Diseases. Biomolecules 2023; 14:5. [PMID: 38275746 PMCID: PMC10813293 DOI: 10.3390/biom14010005] [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: 10/07/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.
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Affiliation(s)
- Marcello Seppi
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Jacopo Pasqualini
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
| | - Sonia Facchin
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Edoardo Vincenzo Savarino
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), University of Padua, Via Giustiniani 2, 35121 Padua, Italy; (S.F.); (E.V.S.)
| | - Samir Suweis
- Laboratory of Interdisciplinary Physics (LIPh), Physics and Astronomy Department, University of Padua, Via Marzolo 8, 35131 Padua, Italy; (M.S.); (J.P.)
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15
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Sun Y, Tang H, Du S, Chen Y, Ou Z, Zhang M, Chen Z, Tang Z, Zhang D, Chen T, Xu Y, Li J, Norback D, Hashim JH, Hashim Z, Shao J, Fu X, Zhao Z. Indoor metabolites and chemicals outperform microbiome in classifying childhood asthma and allergic rhinitis. ECO-ENVIRONMENT & HEALTH (ONLINE) 2023; 2:208-218. [PMID: 38435359 PMCID: PMC10902507 DOI: 10.1016/j.eehl.2023.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 03/05/2024]
Abstract
Indoor microorganisms impact asthma and allergic rhinitis (AR), but the associated microbial taxa often vary extensively due to climate and geographical variations. To provide more consistent environmental assessments, new perspectives on microbial exposure for asthma and AR are needed. Home dust from 97 cases (32 asthma alone, 37 AR alone, 28 comorbidity) and 52 age- and gender-matched controls in Shanghai, China, were analyzed using high-throughput shotgun metagenomic sequencing and liquid chromatography-mass spectrometry. Homes of healthy children were enriched with environmental microbes, including Paracoccus, Pseudomonas, and Psychrobacter, and metabolites like keto acids, indoles, pyridines, and flavonoids (astragalin, hesperidin) (False Discovery Rate < 0.05). A neural network co-occurrence probability analysis revealed that environmental microorganisms were involved in producing these keto acids, indoles, and pyridines. Conversely, homes of diseased children were enriched with mycotoxins and synthetic chemicals, including herbicides, insecticides, and food/cosmetic additives. Using a random forest model, characteristic metabolites and microorganisms in Shanghai homes were used to classify high and low prevalence of asthma/AR in an independent dataset in Malaysian schools (N = 1290). Indoor metabolites achieved an average accuracy of 74.9% and 77.1% in differentiating schools with high and low prevalence of asthma and AR, respectively, whereas indoor microorganisms only achieved 51.0% and 59.5%, respectively. These results suggest that indoor metabolites and chemicals rather than indoor microbiome are potentially superior environmental indicators for childhood asthma and AR. This study extends the traditional risk assessment focusing on allergens or air pollutants in childhood asthma and AR, thereby revealing potential novel intervention strategies for these diseases.
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Affiliation(s)
- Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hao Tang
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Shuang Du
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Yang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhuoru Chen
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Zhiwei Tang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Dongjun Zhang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tianyi Chen
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Yanyi Xu
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Jiufeng Li
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
| | - Dan Norback
- Department of Medical Sciences, Uppsala University, Uppsala SE-751, Sweden
| | - Jamal Hisham Hashim
- Department of Environmental Health, Faculty of Health Sciences, Universiti Selangor, Shah Alam 40000, Malaysia
| | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Malaysia
| | - Jie Shao
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhuohui Zhao
- Department of Environmental Health, School of Public Health, Fudan University, NHC Key Laboratory of Health Technology Assessment (Fudan University), Shanghai 200032, China
- Key Laboratory of Public Health Safety of the Ministry of Education, Shanghai Typhoon Institute/CMA, Shanghai Key Laboratory of Meteorology and Health, Shanghai 200030, China
- IRDR International Center of Excellence on Risk Interconnectivity and Governance on Weather/Climate Extremes Impact and Public Health, Fudan University, Shanghai 200438, China
- WMO/IGAC MAP-AQ Asian Office Shanghai, Fudan University, Shanghai 200438, China
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16
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Hurle GR, Brainard J, Tyler KM. Microbiome diversity is a modifiable virulence factor for cryptosporidiosis. Virulence 2023; 14:2273004. [PMID: 37872759 PMCID: PMC10653618 DOI: 10.1080/21505594.2023.2273004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/15/2023] [Indexed: 10/25/2023] Open
Abstract
Cryptosporidium spp. infection causes significant disease in immunosuppressed individuals and children under the age of 5 years. The severity of the pathological presentation of cryptosporidiosis is a function of the host and parasite genotypes, host immune status, and the enteric environment or microbiome of the host. Cryptosporidiosis often presents with abdominal pain and severe diarrhoea and is associated with intestinal dysbiosis and inflammation. Our systematic analysis of the available literature revealed that bacterial diversity is reduced during infection in larger animal models, lending support to recent studies which indicate that the use of probiotics or the presence of a naturally diverse gut microbiome can prevent or minimise pathology caused by gastrointestinal pathogens. In summary, we present evidence that the presence of a diverse gut microbiome, natural or induced, reduces both symptomatic pathology and oocyst output.
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Affiliation(s)
| | - Julii Brainard
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Kevin. M. Tyler
- Norwich Medical School, University of East Anglia, Norwich, UK
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17
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Le D, Chambers MM, Mercado K, Gutowski CJ. Characterization of the gut microbiome in an osteosarcoma mouse model. J Orthop Res 2023; 41:2730-2739. [PMID: 37246455 DOI: 10.1002/jor.25635] [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: 04/28/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023]
Abstract
Compelling evidence has mounted surrounding the relationship between the gut microbiome and many intestinal and extraintestinal cancers. Few studies exist investigating the relationship between the gut microbiome and sarcoma. We hypothesize that the presence of distant osteosarcoma induces change to the profile of flora within the mouse. Twelve mice were used for this experiment: six were sedated and received an injection of human osteosarcoma cells into the flank, while six served as controls. Baseline stool and weight were collected. Tumor size and mouse weight were recorded weekly, and stool samples were collected and stored. Fecal microbiomes of the mice were profiled by 16S rRNA gene sequencing and analyzed for alpha diversity, relative abundances of microbial taxa, and abundance of specific bacteria at different time points. Alpha diversity was increased in the osteosarcoma group compared with the control group. The family Lachnospiraceae had the second strongest negative net average change in relative abundance over time in the osteosarcoma group whereas it had a positive net average change in the control group. An increased Firmicutes/Bacteroidota (F/B) ratio was observed in the osteosarcoma group relative to the control mice. These differences suggest that there may be an interplay between the gut microbiome and osteosarcoma. Clinical significance: Due to the paucity of literature available, our work can support novel research on this relationship and the development of new, personalized treatments for osteosarcoma.
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Affiliation(s)
- David Le
- Department of Orthopaedic Surgery, Inspira Medical Center, Vineland, New Jersey, USA
| | | | - Kayla Mercado
- Department of Orthopaedic Surgery, Cooper University Healthcare, Camden, New Jersey, USA
| | - Christina J Gutowski
- Cooper Medical School of Rowan University, Camden, New Jersey, USA
- Department of Orthopaedic Surgery, Cooper University Healthcare, Camden, New Jersey, USA
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18
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Loria-Kohen V, Montiel Fernández N, López-Plaza B, Aparicio A. [Anorexia nervosa, microbiota and brain]. NUTR HOSP 2023; 40:46-50. [PMID: 37929904 DOI: 10.20960/nh.04955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Introduction Anorexia nervosa (AN) is a psychiatric disease with a high prevalence and comorbidities, characterized by a low response rate to treatment. It is considered as a multifactorial disease. In recent years, the focus has been placed on the presence of intestinal dysbiosis and its possible involvement as a causal factor as well as an alternative treatment. The objective of this work has been to review the current state of knowledge of alterations in the intestinal microbiota identified in patients with AN and the possibility of using probiotics as a therapeutic alternative. Significant changes in the diversity of species associated with weight loss have been described that could favor the perpetuation of the disorder, and that would explain many of the nutritional, gastrointestinal, psychological, and cognitive alterations present in these patients. The use of probiotics, still little studied in patients with AN, sheds some light on this matter to improve the treatment response, always hand in hand with conventional treatments.
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Affiliation(s)
- Viviana Loria-Kohen
- Departamento de Nutrición y Ciencia de los Alimentos. Facultad de Farmacia. Universidad Complutense de Madrid. Grupo de Investigación VALORNUT-UCM (920030)
| | - Natalia Montiel Fernández
- Máster Universitario en Nutrición Clínica. Universidad Europea. Facultad de Ciencias Biomédicas y de la Salud
| | - Bricia López-Plaza
- Instituto de Investigación Sanitaria La Paz (IdiPAZ). Hospital Universitario La Paz
| | - Aránzazu Aparicio
- Departamento de Nutrición y Ciencia de los Alimentos. Facultad de Farmacia. Universidad Complutense de Madrid. Grupo de Investigación VALORNUT-UCM (920030). IdISSC
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19
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Clough J, Schwab S, Mikac K. Gut Microbiome Profiling of the Endangered Southern Greater Glider ( Petauroides volans) after the 2019-2020 Australian Megafire. Animals (Basel) 2023; 13:3583. [PMID: 38003202 PMCID: PMC10668662 DOI: 10.3390/ani13223583] [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: 10/27/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.
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Affiliation(s)
- Jordyn Clough
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
| | - Sibylle Schwab
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Katarina Mikac
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia;
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20
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Song S, Shon J, Yang WR, Kang HB, Kim KH, Park JY, Lee S, Baik SY, Lee KR, Park YJ. Short-Term Effects of Weight-Loss Meal Replacement Programs with Various Macronutrient Distributions on Gut Microbiome and Metabolic Parameters: A Pilot Study. Nutrients 2023; 15:4744. [PMID: 38004139 PMCID: PMC10675061 DOI: 10.3390/nu15224744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
It has emerged the gut microbiome is crucially linked to metabolic health and obesity. Macronutrient distribution has been discussed as a key parameter in weight-loss programs, but little is known about its impact on the gut microbiome. We investigated the effects of weight-loss meal replacement programs with different macronutrient ratios on the gut microbiota and metabolic parameters in subjects with overweight and obesity. Three low-calorie meal replacement programs with different ratios of carbohydrates, proteins, and lipids were designed: a balanced diet (Group B, 60:15:30), a high-lipid-low-carbohydrate diet (Group F, 35:20:55), and a protein-enriched diet (Group P, 40:25:35). Sixty overweight or obese participants were provided with the meals twice daily for 3 weeks. In all groups, diet intervention resulted in reduced body weight and BMI. The relative abundance of Bacteroidetes and Firmicutes phyla decreased and increased, respectively, which increased the Firmicutes/Bacteroidetes (F/B) ratio in all subjects, particularly in Groups B and P. Alpha- and beta-diversity were augmented at the phylum level in Group P. In conclusion, short-term interventions with weight-loss meal replacement programs increased butyrate-producing bacteria and the F/B ratio. Moreover, the protein-enriched diet significantly increased alpha- and beta-diversity compared to the balanced diet and the high-lipid-low-carbohydrate diet.
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Affiliation(s)
- Seungmin Song
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jinyoung Shon
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Woo-ri Yang
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Han-Bit Kang
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Keun-Ha Kim
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Ju-Yeon Park
- Hyundai Greenfood Greating Laboratory, Yongin-si 16827, Republic of Korea
| | - Sanghoo Lee
- SCL Healthcare Inc., Yongin-si 16954, Republic of Korea
| | - Sae Yun Baik
- Hanaro Medical Foundation, Seoul 03159, Republic of Korea
| | - Kyoung-Ryul Lee
- SCL Healthcare Inc., Yongin-si 16954, Republic of Korea
- Hanaro Medical Foundation, Seoul 03159, Republic of Korea
| | - Yoon Jung Park
- Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Republic of Korea
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21
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Guerrini M, Tanini D, Vannini C, Barbanera F. Wild Avian Gut Microbiome at a Small Spatial Scale: A Study from a Mediterranean Island Population of Alectoris rufa. Animals (Basel) 2023; 13:3341. [PMID: 37958097 PMCID: PMC10648672 DOI: 10.3390/ani13213341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
This research is one of the few comparative descriptions at an intraspecific level of wild non-passerine microbiomes. We investigated for the first time the gut microbiome of red-legged partridges (Alectoris rufa) using fecal pellets in order to provide a more informed management. We focused on a small Italian population consisting of two demes (WEST, EAST) separated by about 20 km on the opposite sides of Elba Island. Given the small spatial scale, we set up a sampling protocol to minimize contamination from environmental bacteria, as well as differences due to variations in-among others-habitat, season, and age of feces, that could possibly affect the investigation of the three Elban sites. We found a significant divergence between the WEST and EAST Elban subpopulations in terms of microbial composition and alpha diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher diversity in western than in eastern partridges. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. We suggest that the two subpopulations should be treated as distinct management units.
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Affiliation(s)
| | | | - Claudia Vannini
- Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy (F.B.)
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22
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Aboushaala K, Wong AYL, Barajas JN, Lim P, Al-Harthi L, Chee A, Forsyth CB, Oh CD, Toro SJ, Williams FMK, An HS, Samartzis D. The Human Microbiome and Its Role in Musculoskeletal Disorders. Genes (Basel) 2023; 14:1937. [PMID: 37895286 PMCID: PMC10606932 DOI: 10.3390/genes14101937] [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: 09/18/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Musculoskeletal diseases (MSDs) are characterized as injuries and illnesses that affect the musculoskeletal system. MSDs affect every population worldwide and are associated with substantial global burden. Variations in the makeup of the gut microbiota may be related to chronic MSDs. There is growing interest in exploring potential connections between chronic MSDs and variations in the composition of gut microbiota. The human microbiota is a complex community consisting of viruses, archaea, bacteria, and eukaryotes, both inside and outside of the human body. These microorganisms play crucial roles in influencing human physiology, impacting metabolic and immunological systems in health and disease. Different body areas host specific types of microorganisms, with facultative anaerobes dominating the gastrointestinal tract (able to thrive with or without oxygen), while strict aerobes prevail in the nasal cavity, respiratory tract, and skin surfaces (requiring oxygen for development). Together with the immune system, these bacteria have coevolved throughout time, forming complex biological relationships. Changes in the microbial ecology of the gut may have a big impact on health and can help illnesses develop. These changes are frequently impacted by lifestyle choices and underlying medical disorders. The potential for safety, expenses, and efficacy of microbiota-based medicines, even with occasional delivery, has attracted interest. They are, therefore, a desirable candidate for treating MSDs that are chronic and that may have variable progression patterns. As such, the following is a narrative review to address the role of the human microbiome as it relates to MSDs.
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Affiliation(s)
- Khaled Aboushaala
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Arnold Y. L. Wong
- Department of Rehabilitation Sciences, The Hong Kong Polytechnic University, Hong Kong SAR, China;
| | - Juan Nicolas Barajas
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Perry Lim
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA;
| | - Ana Chee
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Christopher B. Forsyth
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA;
| | - Chun-do Oh
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Sheila J. Toro
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | | | - Howard S. An
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
| | - Dino Samartzis
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL 60612, USA; (K.A.); (J.N.B.); (P.L.); (A.C.); (C.-d.O.); (S.J.T.); (H.S.A.)
- International Spine Research and Innovation Initiative, Rush University Medical Center, Chicago, IL 60612, USA
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23
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Tao R, Liu S, Crawford J, Tao F. Gut-Brain Crosstalk and the Central Mechanisms of Orofacial Pain. Brain Sci 2023; 13:1456. [PMID: 37891825 PMCID: PMC10605055 DOI: 10.3390/brainsci13101456] [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: 08/21/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Accumulated evidence has demonstrated that the gut microbiome can contribute to pain modulation through the microbiome-gut-brain axis. Various relevant microbiome metabolites in the gut are involved in the regulation of pain signaling in the central nervous system. In this review, we summarize recent advances in gut-brain interactions by which the microbiome metabolites modulate pain, with a focus on orofacial pain, and we further discuss the role of gut-brain crosstalk in the central mechanisms of orofacial pain whereby the gut microbiome modulates orofacial pain via the vagus nerve-mediated direct pathway and the gut metabolites/molecules-mediated indirect pathway. The direct and indirect pathways both contribute to the central regulation of orofacial pain through different brain structures (such as the nucleus tractus solitarius and the parabrachial nucleus) and signaling transmission across the blood-brain barrier, respectively. Understanding the gut microbiome-regulated pain mechanisms in the brain could help us to develop non-opioid novel therapies for orofacial pain.
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Affiliation(s)
| | | | | | - Feng Tao
- Department of Biomedical Sciences, Texas A&M University School of Dentistry, 3302 Gaston Ave., Dallas, TX 75246, USA
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24
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Tsuji M, Tanaka N, Koike H, Sato Y, Shimoyama Y, Itoh A. Various Organ Damages in Rats with Fetal Growth Restriction and Their Slight Attenuation by Bifidobacterium breve Supplementation. Life (Basel) 2023; 13:2005. [PMID: 37895387 PMCID: PMC10607936 DOI: 10.3390/life13102005] [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: 08/05/2023] [Revised: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Children with fetal growth restriction (FGR) and its resultant low birthweight (LBW) are at a higher risk of developing various health problems later in life, including renal diseases, metabolic syndrome, and sarcopenia. The mechanism through which LBW caused by intrauterine hypoperfusion leads to these health problems has not been properly investigated. Oral supplementation with probiotics is expected to reduce these risks in children. In the present study, rat pups born with FGR-LBW after mild intrauterine hypoperfusion were supplemented with either Bifidobacterium breve (B. breve) or a vehicle from postnatal day 1 (P1) to P21. Splanchnic organs and skeletal muscles were evaluated at six weeks of age. Compared with the sham group, the LBW-vehicle group presented significant changes as follows: overgrowth from infancy to childhood; lighter weight of the liver, kidneys, and gastrocnemius and plantaris muscles; reduced height of villi in the ileum; and increased depth of crypts in the jejunum. Some of these changes were milder in the LBW-B.breve group. In conclusion, this rat model could be useful for investigating the mechanisms of how FGR-LBW leads to future health problems and for developing interventions for these problems. Supplementation with B. breve in early life may modestly attenuate these problems.
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Affiliation(s)
- Masahiro Tsuji
- Department of Food and Nutrition, Kyoto Women’s University, Kyoto 605-8501, Japan
| | - Nao Tanaka
- Department of Food and Nutrition, Kyoto Women’s University, Kyoto 605-8501, Japan
| | - Hitomi Koike
- Department of Food and Nutrition, Kyoto Women’s University, Kyoto 605-8501, Japan
| | - Yoshiaki Sato
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, Nagoya 466-8560, Japan;
| | - Yoshie Shimoyama
- Department of Pathology, Nagoya University Hospital, Nagoya 466-8560, Japan
| | - Ayaka Itoh
- Department of Food and Nutrition, Kyoto Women’s University, Kyoto 605-8501, Japan
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25
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Ke S, Xiao Y, Weiss ST, Chen X, Kelly CP, Liu YY. A computational method to dissect colonization resistance of the gut microbiota against pathogens. CELL REPORTS METHODS 2023; 3:100576. [PMID: 37751698 PMCID: PMC10545914 DOI: 10.1016/j.crmeth.2023.100576] [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: 12/14/2022] [Revised: 05/09/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023]
Abstract
The mammalian gut microbiome protects the host through colonization resistance (CR) against the incursion of exogenous and often harmful microorganisms, but identifying the exact microbes responsible for the gut microbiota-mediated CR against a particular pathogen remains a challenge. To address this limitation, we developed a computational method: generalized microbe-phenotype triangulation (GMPT). We first systematically validated GMPT using a classical population dynamics model in community ecology and demonstrated its superiority over baseline methods. We then tested GMPT on simulated data generated from the ecological network inferred from a real community (GnotoComplex microflora) and real microbiome data on two mouse studies on Clostridioides difficile infection. We demonstrated GMPT's ability to streamline the discovery of microbes that are potentially responsible for microbiota-mediated CR against pathogens. GMPT holds promise to advance our understanding of CR mechanisms and facilitate the rational design of microbiome-based therapies for preventing and treating enteric infections.
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Affiliation(s)
- Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yandong Xiao
- College of System Engineering, National University of Defense Technology, Changsha, Hunan 410073, China
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xinhua Chen
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ciarán P Kelly
- Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
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26
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Kang D, Wang X, Wang J. Intervention study of tai chi training on the intestinal flora of college student basketball players. Medicine (Baltimore) 2023; 102:e35044. [PMID: 37682169 PMCID: PMC10489434 DOI: 10.1097/md.0000000000035044] [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] [Received: 10/03/2022] [Accepted: 08/11/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND In recent years, the interactions between host and host-associated gut flora have received increasingly widespread attention. Tai chi is a traditional Chinese exercise, which can significantly benefit adults with health condition. But the studies on the function of intestinal flora and its correlation with tai chi exercise, are limited. In addition, the influence of tai chi on intestinal flora has largely been understudied. In this study, we investigated the changes in intestinal microflora by 16S rRNA sequencing to clarify the specific mechanism of tai chi on the regulation of intestinal flora and seek to formulate a reasonable "exercise prescription." METHODS Design: randomized controlled trial. Participants: thirty college basketball players randomly divided into control (n = 15) and test (n = 15) groups. Intervention: experimental group practiced 24-style simplified tai chi ≥ 6 times/week for 20 weeks. Outcomes: serum biochemical markers, blood pressure, and intestinal microbial composition measured post-intervention. Analysis: intent-to-treat analysis. RESULTS Primary outcomes: after tai chi intervention, the level of high-density lipoprotein cholesterol (1.22 mmol/L) and triglycerides (0.64 mmol/L) were significantly decreased. Secondary outcomes: aspartate transaminase, alanine aminotransferase, total cholesterol, and low-density lipoprotein remained unchanged. Microbiota: α-diversity index significantly increased, particularly with increased Blautia. Blood pressure: test group showed significantly lower diastolic blood pressure (83-95 mm Hg) compared to control. DISCUSSION Considering other markers, increased gut flora diversity during exercise may imply a healthier gut environment. Physical exercise promotes a decrease in the inflammatory process by reducing the levels of bacteria associated with pro-inflammation, such as Proteobacteria. Further research is required to understand the nuanced link between gut flora diversity and exercise intensity. CONCLUSION 24-style simplified tai chi enhances human intestinal flora diversity. Improvements observed in blood lipid profiles and blood pressure levels.
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Affiliation(s)
- Dongyang Kang
- Chengdu Sport University, Chengdu, Sichuan Province, China
- Department of Physical Education, Henan University of Science and Technology, Luoyang, China
| | - Xiaorong Wang
- Department of Physical Education, Luoyang Polytechnic, Luoyang, China
| | - Jiahong Wang
- Department of Physical Education, Soochow University, Suzhou, China
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27
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Han M, Liao W, Dong Y, Fei T, Gai Z. Sustained ameliorative effect of Lactobacillus acidophilus LA85 on dextran sulfate sodium-induced colitis in mice. J Food Sci 2023; 88:3893-3904. [PMID: 37548631 DOI: 10.1111/1750-3841.16723] [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: 03/13/2023] [Revised: 05/28/2023] [Accepted: 07/14/2023] [Indexed: 08/08/2023]
Abstract
Ulcerative colitis (UC) is a type of inflammatory bowel disease associated with immune system dysfunction caused by gut dysbiosis. This study aimed to investigate the alleviating effect of Lactobacillus acidophilus LA85 on colitis and its underlying mechanism using mouse models of dextran sulfate sodium (DSS)-induced UC. The UC mouse models were established by treating C57BL/6J male mice with 2.5% (w/v) DSS in drinking water for 7 days. These mice received supplementation with either L. acidophilus LA85 (1 × 109 colony-forming units/day) or 200 µL of sterile water once daily (LA85-treated and UC model mice, respectively). The disease activity index (DAI), colon length, and histological changes in the colons of mice were then analyzed at Day 21, and the effects of L. acidophilus LA85 on the gut microbiota and serum inflammatory cytokines were also investigated. Compared with the UC model mice, L. acidophilus LA85-treated UC mice showed significant reductions in a variety of colitis symptoms, including weight loss, the DAI score, colon shortening, and colon tissue damage. Lactobacillus acidophilus LA85 supplementation also significantly decreased the serum concentrations of tumor necrosis factor α and interleukin-6 while increasing the serum concentration of IL-10. Furthermore, LA85 supplementation improved the diversity and composition of the gut microbiota, both of which had been decreased by DSS. In particular, L. acidophilus LA85-treated UC mice showed higher relative abundances of Akkermansia and Romboutsia than the UC model mice. These results demonstrate that L. acidophilus LA85 can alleviate inflammatory diseases of the intestine, such as inflammatory bowel disease, by regulating immune responses and restoring the gut microbiota. PRACTICAL APPLICATION: Ulcerative colitis is a type of inflammatory bowel disease caused by imbalance of gut microbiota. This study showed that L. acidophilus LA85 can alleviate DSS-induced colitis in mice through regulation of inflammatory cytokines, protection of intestinal barrier, and regulation of specific gut microbiota. L. acidophilus LA85 is a promising probiotic candidate for the treatment of UC.
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Affiliation(s)
- Mei Han
- Shanghai Business School, Shanghai, China
| | - Wenyan Liao
- State Key Laboratory of Dairy Biotechnology, Technology Center Bright Dairy & Food Co., Ltd., Shanghai, China
| | - Yao Dong
- Department of Research and Development, Wecare Probiotics Co., Ltd., Suzhou, China
| | - Teng Fei
- Department of Research and Development, Wecare Probiotics Co., Ltd., Suzhou, China
| | - Zhonghui Gai
- Department of Research and Development, Wecare Probiotics Co., Ltd., Suzhou, China
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28
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Kishore D, Birzu G, Hu Z, DeLisi C, Korolev KS, Segrè D. Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation. mSystems 2023; 8:e0096122. [PMID: 37338270 PMCID: PMC10469762 DOI: 10.1128/msystems.00961-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/14/2023] [Indexed: 06/21/2023] Open
Abstract
Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes. IMPORTANCE Mapping the interrelationships between different species in a microbial community is important for understanding and controlling their structure and function. The surge in the high-throughput sequencing of microbial communities has led to the creation of thousands of data sets containing information about microbial abundances. These abundances can be transformed into co-occurrence networks, providing a glimpse into the associations within microbiomes. However, processing these data sets to obtain co-occurrence information relies on several complex steps, each of which involves numerous choices of tools and corresponding parameters. These multiple options pose questions about the robustness and uniqueness of the inferred networks. In this study, we address this workflow and provide a systematic analysis of how these choices of tools affect the final network and guidelines on appropriate tool selection for a particular data set. We also develop a consensus network algorithm that helps generate more robust co-occurrence networks based on benchmark synthetic data sets.
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Affiliation(s)
- Dileep Kishore
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Gabriel Birzu
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Zhenjun Hu
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Charles DeLisi
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Kirill S. Korolev
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
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29
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Jensen N, Weiland-Bräuer N, Joel S, Chibani CM, Schmitz RA. The Life Cycle of Aurelia aurita Depends on the Presence of a Microbiome in Polyps Prior to Onset of Strobilation. Microbiol Spectr 2023; 11:e0026223. [PMID: 37378516 PMCID: PMC10433978 DOI: 10.1128/spectrum.00262-23] [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: 01/16/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Aurelia aurita's intricate life cycle alternates between benthic polyp and pelagic medusa stages. The strobilation process, a critical asexual reproduction mechanism in this jellyfish, is severely compromised in the absence of the natural polyp microbiome, with limited production and release of ephyrae. Yet, the recolonization of sterile polyps with a native polyp microbiome can correct this defect. Here, we investigated the precise timing necessary for recolonization as well as the host-associated molecular processes involved. We deciphered that a natural microbiota had to be present in polyps prior to the onset of strobilation to ensure normal asexual reproduction and a successful polyp-to-medusa transition. Providing the native microbiota to sterile polyps after the onset of strobilation failed to restore the normal strobilation process. The absence of a microbiome was associated with decreased transcription of developmental and strobilation genes as monitored by reverse transcription-quantitative PCR. Transcription of these genes was exclusively observed for native polyps and sterile polyps that were recolonized before the initiation of strobilation. We further propose that direct cell contact between the host and its associated bacteria is required for the normal production of offspring. Overall, our findings indicate that the presence of a native microbiome at the polyp stage prior to the onset of strobilation is essential to ensure a normal polyp-to-medusa transition. IMPORTANCE All multicellular organisms are associated with microorganisms that play fundamental roles in the health and fitness of the host. Notably, the native microbiome of the Cnidarian Aurelia aurita is crucial for the asexual reproduction by strobilation. Sterile polyps display malformed strobilae and a halt of ephyrae release, which is restored by recolonizing sterile polyps with a native microbiota. Despite that, little is known about the microbial impact on the strobilation process's timing and molecular consequences. The present study shows that A. aurita's life cycle depends on the presence of the native microbiome at the polyp stage prior to the onset of strobilation to ensure the polyp-to-medusa transition. Moreover, sterile individuals correlate with reduced transcription levels of developmental and strobilation genes, evidencing the microbiome's impact on strobilation on the molecular level. Transcription of strobilation genes was exclusively detected in native polyps and those recolonized before initiating strobilation, suggesting microbiota-dependent gene regulation.
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Affiliation(s)
- Nadin Jensen
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Nancy Weiland-Bräuer
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Shindhuja Joel
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Cynthia Maria Chibani
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
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Hanusch M, He X, Janssen S, Selke J, Trutschnig W, Junker RR. Exploring the Frequency and Distribution of Ecological Non-monotonicity in Associations among Ecosystem Constituents. Ecosystems 2023; 26:1819-1840. [PMID: 38106357 PMCID: PMC10721710 DOI: 10.1007/s10021-023-00867-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/06/2023] [Indexed: 12/19/2023]
Abstract
Complex links between biotic and abiotic constituents are fundamental for the functioning of ecosystems. Although non-monotonic interactions and associations are known to increase the stability, diversity, and productivity of ecosystems, they are frequently ignored by community-level standard statistical approaches. Using the copula-based dependence measure qad, capable of quantifying the directed and asymmetric dependence between variables for all forms of (functional) relationships, we determined the proportion of non-monotonic associations between different constituents of an ecosystem (plants, bacteria, fungi, and environmental parameters). Here, we show that up to 59% of all statistically significant associations are non-monotonic. Further, we show that pairwise associations between plants, bacteria, fungi, and environmental parameters are specifically characterized by their strength and degree of monotonicity, for example, microbe-microbe associations are on average stronger than and differ in degree of non-monotonicity from plant-microbe associations. Considering directed and non-monotonic associations, we extended the concept of ecosystem coupling providing more complete insights into the internal order of ecosystems. Our results emphasize the importance of ecological non-monotonicity in characterizing and understanding ecosystem patterns and processes. Supplementary Information The online version contains supplementary material available at 10.1007/s10021-023-00867-9.
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Affiliation(s)
- Maximilian Hanusch
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Xie He
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Stefan Janssen
- Algorithmic Bioinformatics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Julian Selke
- Algorithmic Bioinformatics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Wolfgang Trutschnig
- Department for Artificial Intelligence & Human Interfaces, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
| | - Robert R. Junker
- Department of Environment and Biodiversity, Paris-Lodron-University Salzburg, 5020 Salzburg, Austria
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043 Marburg, Germany
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Wang C, Ahn J, Tarpey T, Yi SS, Hayes RB, Li H. A microbial causal mediation analytic tool for health disparity and applications in body mass index. MICROBIOME 2023; 11:164. [PMID: 37496080 PMCID: PMC10373330 DOI: 10.1186/s40168-023-01608-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Emerging evidence suggests the potential mediating role of microbiome in health disparities. However, no analytic framework can be directly used to analyze microbiome as a mediator between health disparity and clinical outcome, due to the non-manipulable nature of the exposure and the unique structure of microbiome data, including high dimensionality, sparsity, and compositionality. METHODS Considering the modifiable and quantitative features of the microbiome, we propose a microbial causal mediation model framework, SparseMCMM_HD, to uncover the mediating role of microbiome in health disparities, by depicting a plausible path from a non-manipulable exposure (e.g., ethnicity or region) to the outcome through the microbiome. The proposed SparseMCMM_HD rigorously defines and quantifies the manipulable disparity measure that would be eliminated by equalizing microbiome profiles between comparison and reference groups and innovatively and successfully extends the existing microbial mediation methods, which are originally proposed under potential outcome or counterfactual outcome study design, to address health disparities. RESULTS Through three body mass index (BMI) studies selected from the curatedMetagenomicData 3.4.2 package and the American gut project: China vs. USA, China vs. UK, and Asian or Pacific Islander (API) vs. Caucasian, we exhibit the utility of the proposed SparseMCMM_HD framework for investigating the microbiome's contributions in health disparities. Specifically, BMI exhibits disparities and microbial community diversities are significantly distinctive between reference and comparison groups in all three applications. By employing SparseMCMM_HD, we illustrate that microbiome plays a crucial role in explaining the disparities in BMI between ethnicities or regions. 20.63%, 33.09%, and 25.71% of the overall disparity in BMI in China-USA, China-UK, and API-Caucasian comparisons, respectively, would be eliminated if the between-group microbiome profiles were equalized; and 15, 18, and 16 species are identified to play the mediating role respectively. CONCLUSIONS The proposed SparseMCMM_HD is an effective and validated tool to elucidate the mediating role of microbiome in health disparity. Three BMI applications shed light on the utility of microbiome in reducing BMI disparity by manipulating microbial profiles. Video Abstract.
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Affiliation(s)
- Chan Wang
- Department of Population Health, Division of Biostatistics, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jiyoung Ahn
- Department of Population Health, Division of Epidemiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Thaddeus Tarpey
- Department of Population Health, Division of Biostatistics, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Stella S Yi
- Department of Population Health Section for Health Equity, New York University Grossman School of Medicine, New York, 10016, USA
| | - Richard B Hayes
- Department of Population Health, Division of Epidemiology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Huilin Li
- Department of Population Health, Division of Biostatistics, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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Jaramillo AP, Abaza A, Sid Idris F, Anis H, Vahora I, Moparthi KP, Al Rushaidi MT, Muddam M, Obajeun OA. Diet as an Optional Treatment in Adults With Inflammatory Bowel Disease: A Systematic Review of the Literature. Cureus 2023; 15:e42057. [PMID: 37601990 PMCID: PMC10433035 DOI: 10.7759/cureus.42057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
While the exact cause of IBD is unknown, there are a number of factors that are thought to contribute to its development, including environmental and genetic factors. While exclusive enteral nutrition (EEN) is a promising therapy for Crohn's disease (CD), it is not yet considered a first-line treatment. Additionally, the efficacy of EEN compared to corticosteroid treatment is still being investigated. EEN is suggested as a first-line therapy by which guidelines and in which age groups, as it may differ in pediatric and adult recommendations. Another finding was that dietary changes involving an increase in anti-inflammatory foods and decreased intake of foods high in inflammatory compounds are linked to a beneficial outcome both metabolically and microbiologically in patients with ulcerative colitis (UC) in remission. For relevant medical literature, we examined PubMed/Medline, the Cochrane Library, and Google Scholar as examples of medical databases. The articles were identified, evaluated, and eligibility applied, and nine publications were found. The finished articles investigated the role of several diet alternatives for patients with IBD. Some others have shown that following a normal low-fat diet may be effective in reducing the occurrence of subclinical colitis. The EEN and partial enteral nutrition (PEN) indicated no significant differences between both regimens, but both had good outcomes during active IBD. Other strict diets, such as the specific carbohydrate diet (SCD) versus the Mediterranean diet (MD), demonstrate excellent outcomes in patients with IBD. Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) dietary counseling improves gastrointestinal symptoms and quality of life in IBD patients. Based on the above, we concluded that more studies determining which component of the diet is not clear (proteins, carbs balanced) or diet types are required to establish a particular diet employed as a treatment intervention in these individuals.
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Affiliation(s)
- Arturo P Jaramillo
- General Practice, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Abdelrahman Abaza
- Pathology, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Faten Sid Idris
- Pediatrics, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA
| | - Humna Anis
- Pediatrics, Combined Military Hospital (CMH) Lahore Medical College and Institute of Dentistry, Lahore, PAK
| | - Ilma Vahora
- General Surgery, Saint George's University School of Medicine, Chicago, USA
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Ogilvie CE, Czekster CM. Cyclic dipeptides and the human microbiome: Opportunities and challenges. Bioorg Med Chem 2023; 90:117372. [PMID: 37343497 DOI: 10.1016/j.bmc.2023.117372] [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: 04/08/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
Research into the human microbiome has implicated its constituents in a variety of non-communicable diseases, with certain microbes found to promote health and others leading to dysbiosis and pathogenesis.Microbes communicate and coordinate their behaviour through the secretion of small molecules, such as cyclic dipeptides (CDPs), into their surrounding environment. CDPs are ubiquitous signalling molecules thatexhibit a wide range of biological activities, with particular relevance to human health due to their potential to act as microbiome modulators.
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Affiliation(s)
- Charlene Elizabeth Ogilvie
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.
| | - Clarissa Melo Czekster
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.
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Walker J, Joy AA, Vos LJ, Stenson TH, Mackey JR, Jovel J, Kao D, Madsen KL, Wong GKS. Chemotherapy-induced weight gain in early-stage breast cancer: a prospective matched cohort study reveals associations with inflammation and gut dysbiosis. BMC Med 2023; 21:178. [PMID: 37170273 PMCID: PMC10173591 DOI: 10.1186/s12916-023-02751-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 01/24/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Early-stage breast cancer patients treated with chemotherapy risk the development of metabolic disease and weight gain, which can result in increased morbidity and reduced quality of life in survivorship. We aimed to analyze changes within the gastrointestinal microbiome of early-stage breast cancer patients treated with and without chemotherapy to investigate a potential relationship between dysbiosis, a systemic inflammatory response, and resultant anthropomorphic changes. METHODS We undertook an a priori analysis of serially collected stool and plasma samples from 40 patients with early-stage breast cancer who underwent adjuvant endocrine therapy only, adjuvant chemotherapy only, or both. Gut microbiota were assessed by metagenomic comparison of stool samples following deep sequencing. Inflammatory biomarkers were evaluated by proteomic analysis of plasma and measurement of fecal calprotectin. Body composition was investigated by dual-energy X-ray absorptiometry to determine biomass indices. RESULTS As opposed to treatment with endocrine therapy only, chemotherapy resulted in statistically and clinically significant weight gain and an increase in the android to gynoid ratio of fat distribution. Patients treated with chemotherapy gained an average of 0.15% total mass per month, as opposed to a significantly different loss of 0.19% in those patients who received endocrine-only therapy. Concurrently, a twofold increase in fecal calprotectin occurred after chemotherapy that is indicative of interferon-dependent inflammation and evidence of colonic inflammation. These anthropomorphic and inflammatory changes occurred in concert with a chemotherapy-dependent effect on the gut microbiome as evidenced by a reduction in both the abundance and variety of microbial species. CONCLUSIONS We confirm the association of chemotherapy treatment with weight gain and potential deleterious anthropometric changes and suggest that alterations of bacterial flora may contribute to these phenomena through the induction of systemic inflammation. Consequently, the gut microbiome may be a future target for intervention in preventing chemotherapy-dependent anthropometric changes.
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Affiliation(s)
- John Walker
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H5, Canada.
- Division of Medical Oncology, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada.
| | - Anil Abraham Joy
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H5, Canada
- Division of Medical Oncology, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - Larissa J Vos
- Clinical Trials Unit, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - Trevor H Stenson
- Clinical Trials Unit, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - John R Mackey
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H5, Canada
- Division of Medical Oncology, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - Juan Jovel
- The Applied Genomics Core (TAGC), Faculty of Medicine, University of Alberta, Edmonton, AB, T6G 2X8, Canada
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H5, Canada
| | - Karen L Madsen
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H5, Canada
| | - Gane Ka-Shu Wong
- Division of Gastroenterology, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, T6G 2H5, Canada
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB, T6G 2E9, Canada
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Homan EJ, Bremel RD. Determinants of tumor immune evasion: the role of T cell exposed motif frequency and mutant amino acid exposure. Front Immunol 2023; 14:1155679. [PMID: 37215122 PMCID: PMC10196236 DOI: 10.3389/fimmu.2023.1155679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Few neoepitopes detected in tumor biopsies are immunogenic. Tumor-specific T cell responses require both the presentation of an epitope that differs from wildtype and the presence of T cells with neoepitope-cognate receptors. We show that mutations detected in tumor biopsies result in an increased frequency of rare amino acid combinations compared to the human proteome and gastrointestinal microorganisms. Mutations in a large data set of oncogene and tumor suppressor gene products were compared to wildtype, and to the count of corresponding amino acid motifs in the human proteome and gastrointestinal microbiome. Mutant amino acids in T cell exposed positions of potential neoepitopes consistently generated amino acid motifs that are less common in both proteome reference datasets. Approximately 10% of the mutant amino acid motifs are absent from the human proteome. Motif frequency does not change when mutants were positioned in the MHC anchor positions hidden from T cell receptors. Analysis of neoepitopes in GBM and LUSC cases showed less common T cell exposed motifs, and HLA binding preferentially placing mutant amino acids in an anchor position for both MHC I and MHC II. Cross-presentation of mutant exposed neoepitopes by MHC I and MHC II was particularly uncommon. Review of a tumor mutation dataset known to generate T cell responses showed immunogenic epitopes were those with mutant amino acids exposed to the T cell receptor and with exposed pentamer motifs present in the human and microbiome reference databases. The study illustrates a previously unrecognized mechanism of tumor immune evasion, as rare T cell exposed motifs produced by mutation are less likely to have cognate T cells in the T cell repertoire. The complex interactions of HLA genotype, binding positions, and mutation specific changes in T cell exposed motif underscore the necessity of evaluating potential neoepitopes in each individual patient.
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Calle-García J, Ramayo-Caldas Y, Zingaretti LM, Quintanilla R, Ballester M, Pérez-Enciso M. On the holobiont 'predictome' of immunocompetence in pigs. Genet Sel Evol 2023; 55:29. [PMID: 37127575 PMCID: PMC10150480 DOI: 10.1186/s12711-023-00803-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available. METHODS We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only. RESULTS Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy. CONCLUSIONS Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default.
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Affiliation(s)
- Joan Calle-García
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - María Ballester
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain.
- ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
- Corteva Agriscience, Virtual Location, Bergen op Zoom, Indianapolis, 4611 BB, Netherlands.
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Malcangi G, Patano A, Guglielmo M, Sardano R, Palmieri G, Di Pede C, de Ruvo E, Inchingolo AD, Mancini A, Inchingolo F, Bordea IR, Dipalma G, Inchingolo AM. Precision Medicine in Oral Health and Diseases: A Systematic Review. J Pers Med 2023; 13:jpm13050725. [PMID: 37240895 DOI: 10.3390/jpm13050725] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Precision medicine (PM) is personalized medicine that can develop targeted medical therapies for the individual patient, in which "omics" sciences lead to an integration of data that leads to highly predictive models of the functioning of the individual biological system. They enable rapid diagnosis, assessment of disease dynamics, identification of targeted treatment protocols, and reduction of costs and psychological stress. "Precision dentistry" (DP) is one promising application that need further investigation; the purpose of this paper is therefore to give physicians an overview of the knowledge they need to enhance treatment planning and patient response to therapy. A systematic literature review was conducted on the PubMed, Scopus, and Web of Science databases by analyzing the articles examining the role of precision medicine in dentistry. PM aims to shed light on cancer prevention strategies, by identifying risk factors, and on malformations such as orofacial cleft. Another application is pain management by repurposing drugs created for other diseases to target biochemical mechanisms. The significant heritability of traits regulating bacterial colonization and local inflammatory responses is another result of genomic research, and is useful for DP in the field of caries and periodontitis. This approach may also be useful in the field of orthodontics and regenerative dentistry. The possibility of creating an international network of databases will lead to the diagnosis, prediction, and prevention of disease outbreaks, providing significant economic savings for the world's health care systems.
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Affiliation(s)
- Giuseppina Malcangi
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Assunta Patano
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | | | - Roberta Sardano
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Giulia Palmieri
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Chiara Di Pede
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Elisabetta de Ruvo
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | | | - Antonio Mancini
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
| | - Ioana Roxana Bordea
- Department of Oral Rehabilitation, Faculty of Dentistry, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Gianna Dipalma
- Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70121 Bari, Italy
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Fronton F, Ferchiou S, Caza F, Villemur R, Robert D, St-Pierre Y. Insights into the circulating microbiome of Atlantic and Greenland halibut populations: the role of species-specific and environmental factors. Sci Rep 2023; 13:5971. [PMID: 37045892 PMCID: PMC10097863 DOI: 10.1038/s41598-023-32690-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Establishing long-term microbiome-based monitoring programs is critical for managing and conserving wild fish populations in response to climate change. In most cases, these studies have been conducted on gut and, to a lesser extent, skin (mucus) microbiomes. Here, we exploited the concept of liquid biopsy to study the circulating bacterial microbiome of two Northern halibut species of economic and ecological importance. Amplification and sequencing of the 16S rRNA gene were achieved using a single drop of blood fixed on FTA cards to identify the core blood microbiome of Atlantic and Greenland halibut populations inhabiting the Gulf of St. Lawrence, Canada. We provide evidence that the circulating microbiome DNA (cmDNA) is driven by genetic and environmental factors. More specifically, we found that the circulating microbiome signatures are species-specific and vary according to sex, size, temperature, condition factor, and geographical localization. Overall, our study provides a novel approach for detecting dysbiosis signatures and the risk of disease in wild fish populations for fisheries management, most notably in the context of climate change.
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Affiliation(s)
- Fanny Fronton
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Sophia Ferchiou
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - France Caza
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Richard Villemur
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Dominique Robert
- Institut des Sciences de la Mer, Université du Québec à Rimouski, 310, allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Yves St-Pierre
- INRS-Centre Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada.
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Lan LY, Hong QX, Gao SM, Li Q, You YY, Chen W, Fan PF. Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health. Am J Primatol 2023; 85:e23468. [PMID: 36691713 DOI: 10.1002/ajp.23468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
The gut microbiota plays an integral role in the metabolism and immunity of animal hosts, and provides insights into the health and habitat assessment of threatened animals. The skywalker hoolock gibbon (Hoolock tianxing) is a newly described gibbon species, and is considered an endangered species. Here, we used 16S rRNA amplicon sequencing to describe the fecal bacterial community of skywalker hoolock gibbons from different habitats and in captivity. Fecal samples (n = 5) from two captive gibbons were compared with wild populations (N = 6 gibbons, n = 33 samples). At the phylum level, Spirochetes, Proteobacteria, Firmicutes, Bacteroidetes dominated in captive gibbons, while Firmicutes, Bacteroidetes, and Tenericutes dominated in wild gibbons. At the genus level, captive gibbons were dominated by Treponema-2, followed by Succinivibrio and Cerasicoccus, while wild gibbons were dominated by Anaeroplasma, Prevotellaceae UCG-001, and Erysipelotrichaceae UCG-004. Captive rearing was significantly associated with lower taxonomic alpha-diversity, and different relative abundance of some dominant bacteria compared to wild gibbons. Predicted Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that captive gibbons have significantly lower total pathway diversity and higher relative abundance of bacterial functions involved in "drug resistance: antimicrobial" and "carbohydrate metabolism" than wild gibbons. This study reveals the potential influence of captivity and habitat on the gut bacterial community of gibbons and provides a basis for guiding the conservation management of captive populations.
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Affiliation(s)
- Li-Ying Lan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi-Xuan Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yu-Yan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Piazzesi A, Putignani L. Impact of helminth-microbiome interactions on childhood health and development-A clinical perspective. Parasite Immunol 2023; 45:e12949. [PMID: 36063358 DOI: 10.1111/pim.12949] [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: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/01/2022] [Indexed: 12/01/2022]
Abstract
Humans have co-existed with parasites for virtually the entirety of our existence as a species. Today, nearly one third of the human population is infected with at least one helminthic species, most of which reside in the intestinal tract, where they have co-evolved alongside the human gut microbiota (GM). Appreciation for the interconnected relationship between helminths and GM has increased in recent years. Here, we review the evidence of how helminths and GM can influence various aspects of childhood development and the onset of paediatric diseases. We discuss the emerging evidence of how many of the changes that parasitic worms inflict on their host is enacted through gut microbes. In this light, we argue that helminth-induced microbiota modifications are of great importance in both facing the global challenge of overcoming parasitic infections, and in replicating helminthic protective effects against inflammatory diseases. We propose that deepening our knowledge of helminth-microbiota interactions will uncover novel, safer and more effective therapeutic strategies in combatting an array of childhood disorders.
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Affiliation(s)
- Antonia Piazzesi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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41
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Shan X, Goyal A, Gregor R, Cordero OX. Annotation-free discovery of functional groups in microbial communities. Nat Ecol Evol 2023; 7:716-724. [PMID: 36997739 DOI: 10.1038/s41559-023-02021-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/16/2023] [Indexed: 04/01/2023]
Abstract
Recent studies have shown that microbial communities are composed of groups of functionally cohesive taxa whose abundance is more stable and better-associated with metabolic fluxes than that of any individual taxon. However, identifying these functional groups in a manner that is independent of error-prone functional gene annotations remains a major open problem. Here we tackle this structure-function problem by developing a novel unsupervised approach that coarse-grains taxa into functional groups, solely on the basis of the patterns of statistical variation in species abundances and functional read-outs. We demonstrate the power of this approach on three distinct datasets. On data of replicate microcosms with heterotrophic soil bacteria, our unsupervised algorithm recovered experimentally validated functional groups that divide metabolic labour and remain stable despite large variation in species composition. When leveraged against the ocean microbiome data, our approach discovered a functional group that combines aerobic and anaerobic ammonia oxidizers whose summed abundance tracks closely with nitrate concentrations in the water column. Finally, we show that our framework can enable the detection of species groups that are probably responsible for the production or consumption of metabolites abundant in animal gut microbiomes, serving as a hypothesis-generating tool for mechanistic studies. Overall, this work advances our understanding of structure-function relationships in complex microbiomes and provides a powerful approach to discover functional groups in an objective and systematic manner.
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Affiliation(s)
- Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rachel Gregor
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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42
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Wang AJ, Song D, Hong YM, Liu NN. Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age. Mol Omics 2023; 19:283-296. [PMID: 36916422 DOI: 10.1039/d2mo00288d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.
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Affiliation(s)
- An-Jun Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Dingka Song
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Yue-Mei Hong
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
| | - Ning-Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China.
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43
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Stanaway IB, Wallace JC, Hong S, Wilder CS, Green FH, Tsai J, Knight M, Workman T, Vigoren EM, Smith MN, Griffith WC, Thompson B, Shojaie A, Faustman EM. Alteration of oral microbiome composition in children living with pesticide-exposed farm workers. Int J Hyg Environ Health 2023; 248:114090. [PMID: 36516690 PMCID: PMC9898171 DOI: 10.1016/j.ijheh.2022.114090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/30/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Our prior work shows that azinphos-methyl pesticide exposure is associated with altered oral microbiomes in exposed farmworkers. Here we extend this analysis to show the same association pattern is also evident in their children. Oral buccal swab samples were analyzed at two time points, the apple thinning season in spring-summer 2005 for 78 children and 101 adults and the non-spray season in winter 2006 for 62 children and 82 adults. The pesticide exposure for the children were defined by the farmworker occupation of the cohabitating household adult and the blood azinphos-methyl detection of the cohabitating adult. Oral buccal swab 16S rRNA sequencing determined taxonomic microbiota proportional composition from concurrent samples from both adults and children. Analysis of the identified bacteria showed significant proportional changes for 12 of 23 common oral microbiome genera in association with azinphos-methyl detection and farmworker occupation. The most common significantly altered genera had reductions in the abundance of Streptococcus, suggesting an anti-microbial effect of the pesticide. Principal component analysis of the microbiome identified two primary clusters, with association of principal component 1 to azinphos-methyl blood detection and farmworker occupational status of the household. The children's buccal microbiota composition clustered with their household adult in ∼95% of the households. Household adult farmworker occupation and household pesticide exposure is associated with significant alterations in their children's oral microbiome composition. This suggests that parental occupational exposure and pesticide take-home exposure pathways elicit alteration of their children's microbiomes.
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Affiliation(s)
- Ian B Stanaway
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - James C Wallace
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Sungwoo Hong
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Carly S Wilder
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Foad H Green
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Jesse Tsai
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Misty Knight
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Tomomi Workman
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Eric M Vigoren
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Marissa N Smith
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - William C Griffith
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Beti Thompson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine M Faustman
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
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Kang HJ, Chargo N, Chennupati S, Neugebauer K, Cho JY, Quinn R, McCabe LR, Parameswaran N. Korean Red Ginseng extract treatment prevents post-antibiotic dysbiosis-induced bone loss in mice. J Ginseng Res 2023; 47:265-273. [PMID: 36926616 PMCID: PMC10014174 DOI: 10.1016/j.jgr.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/18/2022] [Accepted: 08/25/2022] [Indexed: 11/27/2022] Open
Abstract
Background The intestinal microbiota is an important regulator of bone health. In previous studies we have shown that intestinal microbiota dysbiosis, induced by treatment with broad spectrum antibiotics (ABX) followed by natural repopulation, results in gut barrier dysfunction and bone loss. We have also shown that treatment with probiotics or a gut barrier enhancer can inhibit dysbiosis-induced bone loss. The overall goal of this project was to test the effect of Korean Red Ginseng (KRG) extract on bone and gut health using antibiotics (ABX) dysbiosis-induced bone loss model in mice. Methods Adult male mice (Balb/C, 12-week old) were administered broad spectrum antibiotics (ampicillin and neomycin) for 2 weeks followed by 4 weeks of natural repopulation. During this 4-week period, mice were treated with vehicle (water) or KRG extract. Other controls included mice that did not receive either antibiotics or KRG extract and mice that received only KRG extract. At the end of the experiments, we assessed various parameters to assess bone, microbiota and in vivo intestinal permeability. Results Consistent with our previous results, post-ABX- dysbiosis led to significant bone loss. Importantly, this was associated with a decrease in gut microbiota alpha diversity and an increase in intestinal permeability. All these effects including bone loss were prevented by KRG extract treatment. Furthermore, our studies identified multiple genera including Lactobacillus and rc4-4 as well as Alistipes finegoldii to be potentially linked to the effect of KRG extract on gut-bone axis. Conclusion Together, our results demonstrate that KRG extract regulates the gut-bone axis and is effective at preventing dysbiosis-induced bone loss in mice.
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Affiliation(s)
- Ho Jun Kang
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Nicholas Chargo
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Soumya Chennupati
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Kerri Neugebauer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jae Youl Cho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Robert Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Laura R McCabe
- Department of Physiology, Michigan State University, East Lansing, MI, USA.,Department of Radiology, Michigan State University, East Lansing, MI, USA
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45
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Bonvegna S, Cilia R. Disease mechanisms as subtypes: Microbiome. HANDBOOK OF CLINICAL NEUROLOGY 2023; 193:107-131. [PMID: 36803806 DOI: 10.1016/b978-0-323-85555-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Abnormalities in gut microbiota have been suggested to be involved in the pathophysiology and progression of Parkinson's disease (PD). Gastrointestinal nonmotor symptoms often precede the onset of motor features in PD, suggesting a role for gut dysbiosis in neuroinflammation and α-synuclein (α-syn) aggregation. In the first part of this chapter, we analyze critical features of healthy gut microbiota and factors (environmental and genetic) that modify its composition. In the second part, we focus on the mechanisms underlying the gut dysbiosis and how it alters anatomically and functionally the mucosal barrier, triggering neuroinflammation and subsequently α-syn aggregation. In the third part, we describe the most common alterations in the gut microbiota of PD patients, dividing the gastrointestinal system in higher and lower tract to examine the association between microbiota abnormalities and clinical features. In the final section, we report on current and future therapeutic approaches to gut dysbiosis aiming to either reduce the risk for PD, modify the disease course, or improve the pharmacokinetic profile of dopaminergic therapies. We also suggest that further studies will be needed to clarify the role of the microbiome in PD subtyping and of pharmacological and nonpharmacological interventions in modifying specific microbiota profiles in individualizing disease-modifying treatments in PD.
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Affiliation(s)
- Salvatore Bonvegna
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy
| | - Roberto Cilia
- Fondazione IRCCS Istituto Neurologico Carlo Besta, Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Milan, Italy.
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46
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Raes J. Nifty new tools for microbiome treatment design. Nat Rev Gastroenterol Hepatol 2023; 20:77-78. [PMID: 36609547 DOI: 10.1038/s41575-022-00735-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jeroen Raes
- Rega Institute, KU Leuven, Leuven, Belgium. .,Center for Microbiology, VIB, Leuven, Belgium.
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47
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Sharma S, Hegde P, Panda S, Orimoloye MO, Aldrich CC. Drugging the microbiome: targeting small microbiome molecules. Curr Opin Microbiol 2023; 71:102234. [PMID: 36399893 DOI: 10.1016/j.mib.2022.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
The human microbiome represents a large and diverse collection of microbes that plays an integral role in human physiology and pathophysiology through interactions with the host and within the microbial community. While early work exploring links between microbiome signatures and diseases states has been associative, emerging evidence demonstrates the metabolic products of the human microbiome have more proximal causal effects on disease phenotypes. The therapeutic implications of this shift are profound as manipulation of the microbiome by the administration of live biotherapeutics, ongoing, can now be pursued alongside research efforts toward describing inhibitors of key microbiome enzymes involved in the biosynthesis of metabolites implicated in various disease states and processing of host-derived metabolites. With growing interest in 'drugging the microbiome', we review few notable microbial metabolites for which traditional drug-development campaigns have yielded compounds with therapeutic promise.
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Affiliation(s)
- Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Subhankar Panda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA.
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48
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Abstract
Studies of the human microbiome share both technical and conceptual similarities with genome-wide association studies and genetic epidemiology. However, the microbiome has many features that differ from genomes, such as its temporal and spatial variability, highly distinct genetic architecture and person-to-person variation. Moreover, there are various potential mechanisms by which distinct aspects of the human microbiome can relate to health outcomes. Recent advances, including next-generation sequencing and the proliferation of multi-omic data types, have enabled the exploration of the mechanisms that connect microbial communities to human health. Here, we review the ways in which features of the microbiome at various body sites can influence health outcomes, and we describe emerging opportunities and future directions for advanced microbiome epidemiology.
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49
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Mildau K, te Beest DE, Engel B, Gort G, Lambert J, Swinkels SN, van Eeuwijk F. Pairwise ratio-based differential abundance analysis of infant microbiome 16S sequencing data. NAR Genom Bioinform 2023; 5:lqad001. [PMID: 36685726 PMCID: PMC9853100 DOI: 10.1093/nargab/lqad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/25/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Differential abundance analysis of infant 16S microbial sequencing data is complicated by challenging data properties, including high sparsity, extreme dispersion and the relative nature of the information contained within the data. In this study, we propose a pairwise ratio analysis that uses the compositional data analysis principle of subcompositional coherence and merges it with a beta-binomial regression model. The resulting method provides a flexible and easily interpretable approach to infant 16S sequencing data differential abundance analysis that does not require zero imputation. We evaluate the proposed method using infant 16S data from clinical trials and demonstrate that the proposed method has the power to detect differences, and demonstrate how its results can be used to gain insights. We further evaluate the method using data-inspired simulations and compare its power against related methods. Our results indicate that power is high for pairwise differential abundance analysis of taxon pairs that have a large abundance. In contrast, results for sparse taxon pairs show a decrease in power and substantial variability in method performance. While our method shows promising performance on well-measured subcompositions, we advise strong filtering steps in order to avoid excessive numbers of underpowered comparisons in practical applications.
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Affiliation(s)
| | | | - Bas Engel
- Biometris, Wageningen University & Research, 6700 HB Wageningen, The Netherlands
| | - Gerrit Gort
- Biometris, Wageningen University & Research, 6700 HB Wageningen, The Netherlands
| | - Jolanda Lambert
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
| | | | - Fred A van Eeuwijk
- Biometris, Wageningen University & Research, 6700 HB Wageningen, The Netherlands
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50
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Wang C, Ahn J, Tarpey T, Yi SS, Hayes RB, Li H. A microbial causal mediation analytic tool for health disparity and applications in body mass index. RESEARCH SQUARE 2023:rs.3.rs-2463503. [PMID: 36712075 PMCID: PMC9882678 DOI: 10.21203/rs.3.rs-2463503/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background: Emerging evidence suggests the potential mediating role of microbiome in health disparities. However, no analytic framework is available to analyze microbiome as a mediator between health disparity and clinical outcome, due to the unique structure of microbiome data, including high dimensionality, sparsity, and compositionality. Methods: Considering the modifiable and quantitative features of microbiome, we propose a microbial causal mediation model framework, SparseMCMM_HD, to uncover the mediating role of microbiome in health disparities, by depicting a plausible path from a non-manipulable exposure (e.g. race or region) to a continuous outcome through microbiome. The proposed SparseMCMM_HD rigorously defines and quantifies the manipulable disparity measure that would be eliminated by equalizing microbiome profiles between comparison and reference groups. Moreover, two tests checking the impact of microbiome on health disparity are proposed. Results: Through three body mass index (BMI) studies selected from the curatedMetagenomicData 3.4.2 package and the American gut project: China vs. USA, China vs. UK, and Asian or Pacific Islander (API) vs. Caucasian, we exhibit the utility of the proposed SparseMCMM_HD framework for investigating microbiome’s contributions in health disparities. Specifically, BMI exhibits disparities and microbial community diversities are significantly distinctive between the reference and comparison groups in all three applications. By employing SparseMCMM_HD, we illustrate that microbiome plays a crucial role in explaining the disparities in BMI between races or regions. 11.99%, 12.90%, and 7.4% of the overall disparity in BMI in China-USA, China-UK, and API-Caucasian comparisons, respectively, would be eliminated if the between-group microbiome profiles were equalized; and 15, 21, and 12 species are identified to play the mediating role respectively. Conclusions: The proposed SparseMCMM_HD is an effective and validated tool to elucidate the mediating role of microbiome in health disparity. Three BMI applications shed light on the utility of microbiome in reducing BMI disparity by manipulating microbial profiles.
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Affiliation(s)
- Chan Wang
- Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, 10016, NY, USA
| | - Jiyoung Ahn
- Division of Epidemiology, Department of Population Health, New York University Grossman School of Medicine, New York, 10016, NY, USA
| | - Thaddeus Tarpey
- Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, 10016, NY, USA
| | - Stella S. Yi
- Department of Population Health Section for Health Equity, New York University Grossman School of Medicine, New York, 10016, USA
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, New York University Grossman School of Medicine, New York, 10016, NY, USA
| | - Huilin Li
- Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, 10016, NY, USA,Correspondence:
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