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Heidrich V, Valles-Colomer M, Segata N. Human microbiome acquisition and transmission. Nat Rev Microbiol 2025:10.1038/s41579-025-01166-x. [PMID: 40119155 DOI: 10.1038/s41579-025-01166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2025] [Indexed: 03/24/2025]
Abstract
As humans, we host personal microbiomes intricately connected to our biology and health. Far from being isolated entities, our microbiomes are dynamically shaped by microbial exchange with the surroundings, in lifelong microbiome acquisition and transmission processes. In this Review, we explore recent studies on how our microbiomes are transmitted, beginning at birth and during interactions with other humans and the environment. We also describe the key methodological aspects of transmission inference, based on the uniqueness of the building blocks of the microbiome - single microbial strains. A better understanding of human microbiome transmission will have implications for studies of microbial host regulation, of microbiome-associated diseases, and for effective microbiome-targeting strategies. Besides exchanging strains with other humans, there is also preliminary evidence we acquire microorganisms from animals and food, and thus a complete understanding of microbiome acquisition and transmission can only be attained by adopting a One Health perspective.
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Affiliation(s)
| | | | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
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Knudsen B, Narain S, Moore BB, Corr PG, Frame LA. Information About the Gut Microbiome's Connection to Health and Disease can Impact Knowledge: Feasibility of an Education-Based Intervention in a General Internal Medicine Clinic. Am J Lifestyle Med 2025:15598276251317129. [PMID: 39897450 PMCID: PMC11786258 DOI: 10.1177/15598276251317129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2025] Open
Abstract
The gut microbiome (gMicrobiome)-a dynamic ecosystem of microorganisms-is emerging as a correlate of healthy lifestyle. Patients may not be aware of this. General Internal Medicine patients completed surveys evaluating gMicrobiome knowledge, lifestyle knowledge, dietary intake, physical activity, sleep, and stress. Surveys were given pre-/post-education (n = 112) and at 1 month follow-up (n = 60). The educational-module comprised a video and handout describing how lifestyle enhances gMicrobiome and health outcomes. Post-educational-module, 9 of 19 (47%) statements showed favorable change in knowledge (P < 0.05). Two statements reached statistical significance at 1-month follow-up: "Exercise influences the types of bacteria present in the digestive system" [7 (12%) to 24 (41%), P = 0.004] and "An inactive lifestyle promotes the growth of healthy types of digestive system bacteria" [12 (20%) to 24 (41%), P = 0.035]. We observed a small but favorable change in knowledge but not behavior. Large lifestyle changes are challenging to adopt, and education alone is necessary but insufficient for change. Our results confirm that education is a viable first step to establish the importance of pursuing lifestyle changes, perhaps moving from pre-contemplation to contemplation. Baseline knowledge in our participants was higher than anticipated, indicating that this intervention may have been too introductory. Future interventions should investigate baseline knowledge.
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Affiliation(s)
- Benjamin Knudsen
- Medical Doctor Program, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Sasha Narain
- Medical Doctor Program, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Brad B. Moore
- Department of Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Patrick G. Corr
- Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- The Resiliency & Well-being Center, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Leigh A. Frame
- Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- The Office of Integrative Medicine and Health, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- The Resiliency & Well-being Center, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
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Azcarate-Peril MA. Has the two decades of research on the gut microbiome resulted in making healthier choices? GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2024; 5:e10. [PMID: 39703542 PMCID: PMC11658936 DOI: 10.1017/gmb.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 07/30/2024] [Accepted: 09/03/2024] [Indexed: 12/21/2024]
Abstract
The gut microbiome is widely recognized for its significant contribution to maintaining human health across all life stages, from infancy to adulthood and beyond. This perspective article focuses on the impacts of well-supported microbiome research on global caesarean delivery rates, breastfeeding practices, and antimicrobial use. The article also explores the impact of dietary choices, particularly those involving ultra-processed foods, on the gut microbiota and their potential contribution to conditions like obesity, metabolic syndrome, and inflammatory diseases. This perspective aims to emphasize the need for updated guidelines and policy interventions to address the increasing global trends of caesarean deliveries, reduced breastfeeding, overuse of antibiotics, and consumption of highly processed foods to counter their adverse effects on gut health.
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Affiliation(s)
- M. Andrea Azcarate-Peril
- Center for Gastrointestinal Biology and Disease (CGIBD), Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, UNC Microbiome Core, University of North Carolina, Chapel Hill, NC, USA
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Nekrasova AI, Kalashnikova IG, Korobeynikova AV, Ashniev GA, Bobrova MM, Bakoev SY, Petryaikina ES, Nekrasov AS, Zagainova AV, Lukashina MV, Tolkacheva LR, Bobrovnitskii IP, Yudin VS, Keskinov AA, Makarov VV, Yudin SM. Characteristics of the Gut Microbiota Composition of the Arctic Zone Residents in the Far Eastern Region. Biomedicines 2024; 12:2472. [PMID: 39595038 PMCID: PMC11591809 DOI: 10.3390/biomedicines12112472] [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: 08/23/2024] [Revised: 10/11/2024] [Accepted: 10/22/2024] [Indexed: 11/28/2024] Open
Abstract
Background. In many studies over the past decade, scientists have made a connection between the composition of gut microbiota and human health. A number of publications have shown that gut bacteria are involved in many metabolic and physiological processes of the organism. The composition of the gut microbiome is unique for each person and is formed under the influence of various factors associated with both the individual characteristics of the body and the characteristics of the environment. Different regional characteristics make it necessary for the body to adapt to certain conditions, including temperature fluctuations. Living in areas with low temperatures, such as the Arctic zone, dictates the need for increased energy consumption, which affects the composition of the gut microbiome. Methods. In our study, an extensive questionnaire was conducted among the participants, where many questions were included about the dietary preferences of the study participants, which allowed them us to further divide them into groups according to their diets. Stool samples were collected from participants from 3 groups: Arctic native, Arctic newcomer and the control group. The next step was the isolation of bacterial DNA and sequencing the 16S rRNA gene. The analysis of the results of the diversity of the intestinal microbiota was carried out both with and without taking into account the dietary preferences of the participants. Results. As a result of comparing the intestinal microbiota obtained from residents of the Arctic zone with the gut microbiota of residents of other regions with a milder climate, significant differences are found. These differences may be related to limited food resources and a reduction in the variety of food products characteristic of this Arctic region. t was also found that representatives of the bacterial families Christensenellaceae and Muribaculaceae dominated the control group, both with traditional nutrition and with a dairy-free diet in comparison with the Arctic groups. The control group was dominated by representatives of the Prevotellaceae, Enterobacteriaceae and Comamonadaceae families compared to the Arctic group (with a traditional diet). The results also show that the number of representatives of the families Desulfovibrionaceae (with traditional diet) and Enterobacteriaceae (with milk-free diet) is growing in the Arctic group. Conclusions. In the course of this work, bacterial families characteristic of people living in the Arc-tic zone of the Far Eastern region of the Russian Federation were identified. Poor diet, difficult climatic conditions, and problems with logistics and medical care can have a strong impact on the health of this population. The main type of diet for the inhabitants of the Arctic is the traditional type of diet. They consume a large number of low-cost products, obtainget animal protein from poultry and canned food, and also eat a small number of fresh vegetables and fruits. Such a diet is due to the social status of the study participants and the climatic and geographical features of the region (difficulties in agriculture). With such a diet, we observe a decrease in representatives of the Christensenellaceae, Muribaculaceae, Eubacteriaceae, and Prevotellaceae families and an increase in representatives of the Enterobacteriaceae and Desulfovibrionaceae families among Arctic residents. This imbalance in the futuremay cause, this population may to develop various diseases in the future, including chronic diseases such as obesity, intestinal dysbiosis, inflammatory bowel diseases, and type 2 diabetes.
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Affiliation(s)
- Alexandra I. Nekrasova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Irina G. Kalashnikova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Anna V. Korobeynikova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - German A. Ashniev
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Maria M. Bobrova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Sirozhdin Yu. Bakoev
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Ekaterina S. Petryaikina
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Alexander S. Nekrasov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Angelika V. Zagainova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Mariya V. Lukashina
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Larisa R. Tolkacheva
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Igor P. Bobrovnitskii
- Federal State Budgetary Scientific Institution “Institute of General Pathology and Pathophysiology”, Baltiyskaya Str., 8, 125315 Moscow, Russia;
- State Scientific Center, the Russian Federation Institute of Biomedical Problems, the Russian Academy of Sciences, Khoroshevskoe Shosse, 76A, 123007 Moscow, Russia
| | - Vladimir S. Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Anton A. Keskinov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Valentin V. Makarov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
| | - Sergey M. Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks”, the Federal Medical and Biological Agency, Pogodinskaya Str., 10/1, 119121 Moscow, Russia; (I.G.K.); (A.V.K.); (G.A.A.); (M.M.B.); (S.Y.B.); (E.S.P.); (A.S.N.); (A.V.Z.); (M.V.L.); (L.R.T.); (V.S.Y.); (A.A.K.); (V.V.M.); (S.M.Y.)
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Carlino N, Blanco-Míguez A, Punčochář M, Mengoni C, Pinto F, Tatti A, Manghi P, Armanini F, Avagliano M, Barcenilla C, Breselge S, Cabrera-Rubio R, Calvete-Torre I, Coakley M, Cobo-Díaz JF, De Filippis F, Dey H, Leech J, Klaassens ES, Knobloch S, O'Neil D, Quijada NM, Sabater C, Skírnisdóttir S, Valentino V, Walsh L, Alvarez-Ordóñez A, Asnicar F, Fackelmann G, Heidrich V, Margolles A, Marteinsson VT, Rota Stabelli O, Wagner M, Ercolini D, Cotter PD, Segata N, Pasolli E. Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell 2024; 187:5775-5795.e15. [PMID: 39214080 DOI: 10.1016/j.cell.2024.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/17/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.
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Affiliation(s)
- Niccolò Carlino
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Aitor Blanco-Míguez
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michal Punčochář
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Claudia Mengoni
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Pinto
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessia Tatti
- Scuola Universitaria Superiore IUSS Pavia, Pavia, Italy; Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, Italy
| | - Paolo Manghi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michele Avagliano
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Coral Barcenilla
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Samuel Breselge
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Biotechnology, Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Inés Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mairéad Coakley
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Hrituraj Dey
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - John Leech
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | | | | | | | - Narciso M Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety, and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria; Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria; Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | | | - Vincenzo Valentino
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Liam Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | | | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Gloria Fackelmann
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Vitor Heidrich
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Viggó Thór Marteinsson
- Microbiology Research Group, Matís, Reykjavík, Iceland; University of Iceland, Faculty of Food Science and Nutrition, Reykjavík, Iceland
| | - Omar Rota Stabelli
- Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All'Adige, Italy
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety, and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria; Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
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Malamitsi-Puchner A, Briana DD, Di Renzo GC. The microbiome in pregnancy and early life-Highlights from the 11th Maria Delivoria-Papadopoulos Perinatal Symposium. Acta Paediatr 2024; 113:2189-2196. [PMID: 38895845 DOI: 10.1111/apa.17328] [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: 04/02/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
This review was based on a symposium that examined novel aspects of the microbiome during pregnancy and early life and explored papers published by the lecturers. For example, it showed that bacterial extracellular vesicles derived from the microbiome harboured in various maternal niches, carried bacterial deoxyribonucleic acid, were isolated from the placenta and may have confounded placental microbiome studies. Maternal diet was responsible for the composition and diversity of breast milk microbiota, and may have shaped the offspring's microbiome and influenced their immune components. Probiotics and antibiotics administered perinatally may have had beneficial but also long-lasting adverse effects on offspring.
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Affiliation(s)
- Ariadne Malamitsi-Puchner
- Neonatal Intensive Care Unit, 3rd Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Despina D Briana
- Neonatal Intensive Care Unit, 3rd Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Gian Carlo Di Renzo
- PREIS School, International and European School of Perinatal, Neonatal and Reproductive Medicine, Florence, Italy
- Department of Obstetrics, Gynecology and Perinatology, I.M. Sechenov First State University of Moscow, Moscow, Russia
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7
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Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, Giordano F, Hadjigeorgiou G, Leeming ER, Lobina M, Masala M, Maschio A, McIver LJ, Pala M, Pitzalis M, Wolf J, Fu J, Zhernakova A, Cacciò SM, Cucca F, Berry SE, Ercolini D, Chan AT, Huttenhower C, Spector TD, Segata N, Asnicar F. Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries. Cell 2024; 187:4554-4570.e18. [PMID: 38981480 DOI: 10.1016/j.cell.2024.06.018] [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: 05/12/2023] [Revised: 02/23/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.
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Affiliation(s)
- Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Hanseul Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alberto Arrè
- Department CIBIO, University of Trento, Trento, Italy; Zoe Ltd, London, UK
| | - Kate M Bermingham
- Zoe Ltd, London, UK; Department of Nutritional Sciences, King's College London, London, UK
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | | | - Emily R Leeming
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Monia Lobina
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tim D Spector
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
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8
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Dubois L, Valles-Colomer M, Ponsero A, Helve O, Andersson S, Kolho KL, Asnicar F, Korpela K, Salonen A, Segata N, de Vos WM. Paternal and induced gut microbiota seeding complement mother-to-infant transmission. Cell Host Microbe 2024; 32:1011-1024.e4. [PMID: 38870892 DOI: 10.1016/j.chom.2024.05.004] [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: 10/15/2023] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess the role of both parents and of induced seeding, we analyzed two longitudinal metagenomic datasets (health and early life microbiota [HELMi]: N = 74 infants, 398 samples, and SECFLOR: N = 7 infants, 35 samples) with cesarean-born infants who received maternal fecal microbiota transplantation (FMT). We found that the father constitutes a stable source of strains for the infant independently of the delivery mode, with the cumulative contribution becoming comparable to that of the mother after 1 year. Maternal FMT increased mother-infant strain sharing in cesarean-born infants, raising the average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate that maternal seeding is partly complemented by that of the father and support the potential of induced seeding to restore potential deviations in this process.
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Affiliation(s)
- Léonard Dubois
- Department CIBIO, University of Trento, 38123 Trento, Italy
| | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, 38123 Trento, Italy; MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Alise Ponsero
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Otto Helve
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland; Department of Health Security, Finnish Institute for Health and Welfare, 0014 Helsinki, Finland
| | - Sture Andersson
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland
| | - Kaija-Leena Kolho
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | | | - Katri Korpela
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Anne Salonen
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, 38123 Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy.
| | - Willem M de Vos
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland; Laboratory of Microbiology, University of Wageningen, 6703 WE Wageningen, the Netherlands.
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9
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Caffrey EB, Sonnenburg JL, Devkota S. Our extended microbiome: The human-relevant metabolites and biology of fermented foods. Cell Metab 2024; 36:684-701. [PMID: 38569469 DOI: 10.1016/j.cmet.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
One of the key modes of microbial metabolism occurring in the gut microbiome is fermentation. This energy-yielding process transforms common macromolecules like polysaccharides and amino acids into a wide variety of chemicals, many of which are relevant to microbe-microbe and microbe-host interactions. Analogous transformations occur during the production of fermented foods, resulting in an abundance of bioactive metabolites. In foods, the products of fermentation can influence food safety and preservation, nutrient availability, and palatability and, once consumed, may impact immune and metabolic status, disease expression, and severity. Human signaling pathways perceive and respond to many of the currently known fermented food metabolites, though expansive chemical novelty remains to be defined. Here we discuss several aspects of fermented food-associated microbes and metabolites, including a condensed history, current understanding of their interactions with hosts and host-resident microbes, connections with commercial probiotics, and opportunities for future research on human health and disease and food sustainability.
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Affiliation(s)
- Elisa B Caffrey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA.
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel Diseases Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Human Microbiome Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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10
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Yang R, Wang H, Chen D, Cai Q, Zhu J, Yuan S, Wang F, Xu X. The effect of in-hospital breast milk intake on the gut microbiota of preterm infants. Clin Nutr ESPEN 2024; 60:146-155. [PMID: 38479903 DOI: 10.1016/j.clnesp.2024.01.020] [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: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 04/13/2024]
Abstract
OBJECTIVE The aim of this study was to explore the effect of in-hospital breast milk intake on the development of early gut microbiota in preterm infants in two dimensions: longitudinal over time and cross-sectional between groups. METHODS Researchers collected preterm infants' general data baseline characteristics, recorded their daily breast milk intake, probiotics, and antibiotics use, and collected their stool specimens at 1st week, 2 nd week, 3rd week and 4th week after birth. The researchers analyzed the effect of breast milk on gut microbiota of preterm infants by bioinformatics methods of intra-group longitudinal variation of gut microbiota structure and diversity in preterm infants and cross-sectional differences between >70 % in-hospital breast milk intake (BM) group and ≤70 % (PF) group. RESULTS A total of 60 preterm infants were included in this study, and a total of 213 stool specimens were retained. BM had statistically different Shannon and Simpson indices between the first and fourth week after admission (P < 0.05), both of them showed a lower diversity in the later week than in the previous week. The Shannon index and Simpson index of BM from week 3 onwards were statistically different from PF (P < 0.05), and the Shannon index and Simpson index of BM were lower than those of PF. Significantly statistical differences (P < 0.05) were found in the beta diversity of gut microbiota in preterm infants as time progressed, and both showed a lower beta diversity in the later week than in the preceding week. The dominant taxa of PF in the first postnatal week were Bifidobacterium animalis, etc., the dominant taxa of BM in the third postnatal week were Clostridium_sensu_stricto _1, etc. CONCLUSIONS: The development and evolution of gut microbiota in preterm infants' in-hospital period was a continuous, non-random process, and similar trends in species composition and changes in gut microbes emerged in preterm infants with different ratio of breast milk intake. In the NICU setting, alpha diversity was lower in preterm infants in the >70 % breast milk intake group than in the ≤70 % group when compared between groups at the same time, which may be related to delayed maturation of gut microbes and represents a more developmental gut time window.
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Affiliation(s)
- Rui Yang
- School of Nursing, Capital Medical University, Beijing, China
| | - Hua Wang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Danqi Chen
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qian Cai
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiajun Zhu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuiqin Yuan
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fang Wang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Xinfen Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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11
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Tian Z, Zhang X, Yao G, Jin J, Zhang T, Sun C, Wang Z, Zhang Q. Intestinal flora and pregnancy complications: Current insights and future prospects. IMETA 2024; 3:e167. [PMID: 38882493 PMCID: PMC11170975 DOI: 10.1002/imt2.167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/22/2023] [Indexed: 06/18/2024]
Abstract
Numerous studies have demonstrated the pivotal roles of intestinal microbiota in many physiopathological processes through complex interactions with the host. As a unique period in a woman's lifespan, pregnancy is characterized by changes in hormones, immunity, and metabolism. The gut microbiota also changes during this period and plays a crucial role in maintaining a healthy pregnancy. Consequently, anomalies in the composition and function of the gut microbiota, namely, gut microbiota dysbiosis, can predispose individuals to various pregnancy complications, posing substantial risks to both maternal and neonatal health. However, there are still many controversies in this field, such as "sterile womb" versus "in utero colonization." Therefore, a thorough understanding of the roles and mechanisms of gut microbiota in pregnancy and its complications is essential to safeguard the health of both mother and child. This review provides a comprehensive overview of the changes in gut microbiota during pregnancy, its abnormalities in common pregnancy complications, and potential etiological implications. It also explores the potential of gut microbiota in diagnosing and treating pregnancy complications and examines the possibility of gut-derived bacteria residing in the uterus/placenta. Our aim is to expand knowledge in maternal and infant health from the gut microbiota perspective, aiding in developing new preventive and therapeutic strategies for pregnancy complications based on intestinal microecology.
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Affiliation(s)
- Zhenyu Tian
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Xinjie Zhang
- Department of Biology University College London London UK
| | - Guixiang Yao
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Jiajia Jin
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Tongxue Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
| | - Chunhua Sun
- Department of Health Management Center, Qilu Hospital, Cheeloo College of Medicine Shandong University Jinan China
| | - Zhe Wang
- Department of Geriatrics Shandong Provincial Hospital Affiliated to Shandong First Medical University Jinan China
| | - Qunye Zhang
- National Key Laboratory for Innovation and Transformation of Luobing Theory; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences; Department of Cardiology Qilu Hospital of Shandong University Jinan China
- Cardiovascular Disease Research Center of Shandong First Medical University Central Hospital Affiliated to Shandong First Medical University Jinan China
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12
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Huang KD, Amend L, Gálvez EJC, Lesker TR, de Oliveira R, Bielecka A, Blanco-Míguez A, Valles-Colomer M, Ruf I, Pasolli E, Buer J, Segata N, Esser S, Strowig T, Kehrmann J. Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices. Cell Rep Med 2024; 5:101426. [PMID: 38366600 PMCID: PMC10982974 DOI: 10.1016/j.xcrm.2024.101426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.
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Affiliation(s)
- Kun D Huang
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - Till-Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Romulo de Oliveira
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; Department of Medicine and Life Sciences, University Pompeu Fabra, Barcelona, Spain
| | - Isabel Ruf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples, Naples, Italy
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Stefan Esser
- Department of Dermatology and Venerology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany; Centre for Individualized Infection Medicine, Hannover, Germany.
| | - Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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13
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Rampelli S, Gallois S, D’Amico F, Turroni S, Fabbrini M, Scicchitano D, Candela M, Henry A. The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods. iScience 2024; 27:109211. [PMID: 38433907 PMCID: PMC10904984 DOI: 10.1016/j.isci.2024.109211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/21/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Sandrine Gallois
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
- Institute of Environmental Science and Technology, ST, 08193 Bellaterra, Spain
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences (DiMeC), Alma Mater Studiorum – University of Bologna, 40138 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum – University of Bologna, 40126 Bologna, Italy
| | - Amanda Henry
- Department of Archaeological Sciences, Faculty of Archaeology, Leiden University, 2311 Leiden, the Netherlands
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14
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Bernabeu M, Cabello-Yeves E, Flores E, Samarra A, Kimberley Summers J, Marina A, Collado MC. Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads. Curr Opin Microbiol 2024; 77:102424. [PMID: 38237429 DOI: 10.1016/j.mib.2023.102424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024]
Abstract
Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area.
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Affiliation(s)
- Manuel Bernabeu
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain.
| | - Elena Cabello-Yeves
- Instituto de Biomedicina de Valencia-Consejo de Investigaciones Científicas (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain.
| | - Eduard Flores
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
| | - Joanna Kimberley Summers
- Wellington Lab, School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom
| | - Alberto Marina
- Instituto de Biomedicina de Valencia-Consejo de Investigaciones Científicas (IBV-CSIC), CIBER de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | - M Carmen Collado
- Institute of Agrochemistry and Food Technology - National Research Council (IATA-CSIC), 46980 Valencia, Spain
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15
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Samarra A, Flores E, Bernabeu M, Cabrera-Rubio R, Bäuerl C, Selma-Royo M, Collado MC. Shaping Microbiota During the First 1000 Days of Life. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1449:1-28. [PMID: 39060728 DOI: 10.1007/978-3-031-58572-2_1] [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: 07/28/2024]
Abstract
Given that the host-microbe interaction is shaped by the immune system response, it is important to understand the key immune system-microbiota relationship during the period from conception to the first years of life. The present work summarizes the available evidence concerning human reproductive microbiota, and also, the microbial colonization during early life, focusing on the potential impact on infant development and health outcomes. Furthermore, we conclude that some dietary strategies including specific probiotics and other-biotics could become potentially valuable tools to modulate the maternal-neonatal microbiota during this early critical window of opportunity for targeted health outcomes throughout the entire lifespan.
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Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Eduard Flores
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Manuel Bernabeu
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Christine Bäuerl
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Marta Selma-Royo
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Paterna-Valencia, Spain.
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