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Truter M, Koopman JE, Jordaan K, Tsamkxao LO, Cowan DA, Underdown SJ, Ramond JB, Rifkin RF. Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome. Cell Rep 2024; 43:113690. [PMID: 38244196 DOI: 10.1016/j.celrep.2024.113690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Juǀ'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|'hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|'hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.
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Affiliation(s)
- Mia Truter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Scientific Computing Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7700, South Africa
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Karen Jordaan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Leon Oma Tsamkxao
- Juǀ'hoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK; Extreme Ecosystem Microbiomics & Ecogenomics (E(2)ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Juǀ'hoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK.
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Heiskanen MA, Aatsinki A, Hakonen P, Kartiosuo N, Munukka E, Lahti L, Keskitalo A, Huovinen P, Niinikoski H, Viikari J, Rönnemaa T, Lagström H, Jula A, Raitakari O, Rovio SP, Pahkala K. Association of Long-Term Habitual Dietary Fiber Intake since Infancy with Gut Microbiota Composition in Young Adulthood. J Nutr 2024; 154:744-754. [PMID: 38219864 DOI: 10.1016/j.tjnut.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Dietary fiber is an important health-promoting component of the diet, which is fermented by the gut microbes that produce metabolites beneficial for the host's health. OBJECTIVES We studied the associations of habitual long-term fiber intake from infancy with gut microbiota composition in young adulthood by leveraging data from the Special Turku Coronary Risk Factor Intervention Project, an infancy-onset 20-y dietary counseling study. METHODS Fiber intake was assessed annually using food diaries from infancy ≤ age 20 y. At age 26 y, the first postintervention follow-up study was conducted including food diaries and fecal sample collection (N = 357). Cumulative dietary fiber intake was assessed as the area under the curve for energy-adjusted fiber intake throughout the study (age 0-26 y). Gut microbiota was profiled using 16S ribosomal ribonucleic acid amplicon sequencing. The primary outcomes were 1) α diversity expressed as the observed richness and Shannon index, 2) β diversity using Bray-Curtis dissimilarity scores, and 3) differential abundance of each microbial taxa with respect to the cumulative energy-adjusted dietary fiber intake. RESULTS Higher cumulative dietary fiber intake was associated with decreased Shannon index (β = -0.019 per unit change in cumulative fiber intake, P = 0.008). Overall microbial community composition was related to the amount of fiber consumed (permutational analysis of variation R2 = 0.005, P = 0.024). The only genus that was increased with higher cumulative fiber intake was butyrate-producing Butyrivibrio (log2 fold-change per unit change in cumulative fiber intake 0.40, adjusted P = 0.023), whereas some other known butyrate producers such as Faecalibacterium and Subdoligranulum were decreased with higher cumulative fiber intake. CONCLUSIONS As early-life nutritional exposures may affect the lifetime microbiota composition and disease risk, this study adds novel information on the associations of long-term dietary fiber intake with the gut microbiota. This trial was registered at clinicaltrials.gov as NCT00223600.
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Affiliation(s)
- Marja A Heiskanen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.
| | - Anna Aatsinki
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Petra Hakonen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Noora Kartiosuo
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Mathematics and Statistics, University of Turku, Turku, Finland
| | - Eveliina Munukka
- Turku Clinical Microbiome Biobank, Department of Clinical Microbiology, Turku University Hospital, Turku, Finland; Institute of Biomedicine, University of Turku, Turku, Finland
| | - Leo Lahti
- Department of Computing, Faculty of Technology, University of Turku, Turku, Finland
| | - Anniina Keskitalo
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Pentti Huovinen
- Institute of Biomedicine, University of Turku, Turku, Finland; Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Harri Niinikoski
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Pediatrics, University of Turku, Turku, Finland
| | - Jorma Viikari
- Department of Medicine, University of Turku, Turku, Finland; Division of Medicine, Turku University Hospital, Turku, Finland
| | - Tapani Rönnemaa
- Department of Medicine, University of Turku, Turku, Finland; Division of Medicine, Turku University Hospital, Turku, Finland
| | - Hanna Lagström
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Public Health, Turku University Hospital, University of Turku, Turku, Finland
| | - Antti Jula
- Department of Public Health Solutions, Institute for Health and Welfare, Turku, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Suvi P Rovio
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Public Health, Turku University Hospital, University of Turku, Turku, Finland
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Paavo Nurmi Centre and Unit for Health and Physical Activity, University of Turku, Turku, Finland
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Manus MB, Sardaro MLS, Dada O, Davis MI, Romoff MR, Torello SG, Ubadigbo E, Wu RC, Miller ES, Amato KR. Interactions with alloparents are associated with the diversity of infant skin and fecal bacterial communities in Chicago, United States. Am J Hum Biol 2023:e23972. [PMID: 37632331 DOI: 10.1002/ajhb.23972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/28/2023] Open
Abstract
INTRODUCTION Social interactions shape the infant microbiome by providing opportunities for caregivers to spread bacteria through physical contact. With most research focused on the impact of maternal-infant contact on the infant gut microbiome, it is unclear how alloparents (i.e., caregivers other than the parents) influence the bacterial communities of infant body sites that are frequently contacted during bouts of caregiving, including the skin. METHODS To begin to understand how allocare may influence the diversity of the infant microbiome, detailed questionnaire data on infant-alloparent relationships and specific allocare behaviors were coupled with skin and fecal microbiome samples (four body sites) from 48 infants living in Chicago, United States. RESULTS Data from 16S rRNA gene amplicon sequencing indicated that infant skin and fecal bacterial diversity showed strong associations (positive and negative) to having female adult alloparents. Alloparental feeding and co-sleeping displayed stronger associations to infant bacterial diversity compared to playing or holding. The associations with allocare behaviors differed in magnitude and direction across infant body sites. Bacterial relative abundances varied by infant-alloparent relationship and breastfeeding status. CONCLUSION This study provides some of the first evidence of an association between allocare and infant skin and fecal bacterial diversity. The results suggest that infants' exposure to bacteria from the social environment may vary based on infant-alloparent relationships and allocare behaviors. Since the microbiome influences immune system development, variation in allocare that impacts the diversity of infant bacterial communities may be an underexplored dimension of the social determinants of health in early life.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maria Luisa Savo Sardaro
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Human Science and Promotion of the Quality of Life, University of San Raffaele, Rome, Italy
| | - Omolola Dada
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maya I Davis
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Melissa R Romoff
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Stephanie G Torello
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Esther Ubadigbo
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Rebecca C Wu
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Emily S Miller
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [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: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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Rural Embodiment and Community Health: an Anthropological Case Study on Biocultural Determinants of Tropical Disease Infection and Immune System Development in the USA. CURRENT TROPICAL MEDICINE REPORTS 2023; 10:26-39. [PMID: 36714157 PMCID: PMC9868515 DOI: 10.1007/s40475-023-00282-z] [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: 12/12/2022] [Indexed: 01/24/2023]
Abstract
Purpose of Review Biocultural methods are critically important for identifying environmental and socioeconomic factors linked with tropical disease risk and outcomes. For example, embodiment theory refers to the process by which lived experiences impact individual biology. Increased exposure to pathogens, chronic psychosocial stress, and unequal resource access are all outcomes linked with discrimination and poverty. Through lived experiences, race and socioeconomic inequality can literally become embodied-get under the skin and affect physiology-impacting immune responses and contributing to lifelong health disparities. Yet, few studies have investigated tropical disease patterns and associated immune function using embodiment theory to understand lasting physiological impacts associated with living in a high-pathogen environment. Recent Findings Here, we use preliminary data drawn from the Rural Embodiment and Community Health (REACH) study to assess whether pathogen exposure and immune stimulation within a sample of children from the Mississippi Delta are associated with household income. We also test whether immune marker levels-assessed with enzyme-linked immunosorbent assays using dried blood spot samples-vary between the REACH sample and a similarly aged nationally representative NHANES sample. Immune marker levels did not differ significantly between REACH participants living below vs. above the federal poverty line, yet immunoglobulin E levels-a marker of macroparasite infection-were higher among REACH study participants compared to the NHANES sample. Summary These results may suggest community-level pathogenic exposures (i.e., parasitic infections) are embodied by REACH participants with implications for long-term immune function, potentially resulting in immune aspects that differ from nationally representative samples. Supplementary Information The online version contains supplementary material available at 10.1007/s40475-023-00282-z.
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Dietary Fiber Intake and Gut Microbiota in Human Health. Microorganisms 2022; 10:microorganisms10122507. [PMID: 36557760 PMCID: PMC9787832 DOI: 10.3390/microorganisms10122507] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Dietary fiber is fermented by the human gut microbiota, producing beneficial microbial metabolites, such as short-chain fatty acids. Over the last few centuries, dietary fiber intake has decreased tremendously, leading to detrimental alternations in the gut microbiota. Such changes in dietary fiber consumption have contributed to the global epidemic of obesity, type 2 diabetes, and other metabolic disorders. The responses of the gut microbiota to the dietary changes are specific to the type, amount, and duration of dietary fiber intake. The intricate interplay between dietary fiber and the gut microbiota may provide clues for optimal intervention strategies for patients with type 2 diabetes and other noncommunicable diseases. In this review, we summarize current evidence regarding dietary fiber intake, gut microbiota modulation, and modification in human health, highlighting the type-specific cutoff thresholds of dietary fiber for gut microbiota and metabolic outcomes.
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Alt KW, Al-Ahmad A, Woelber JP. Nutrition and Health in Human Evolution–Past to Present. Nutrients 2022; 14:nu14173594. [PMID: 36079850 PMCID: PMC9460423 DOI: 10.3390/nu14173594] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022] Open
Abstract
Anyone who wants to understand the biological nature of humans and their special characteristics must look far back into evolutionary history. Today’s way of life is drastically different from that of our ancestors. For almost 99% of human history, gathering and hunting have been the basis of nutrition. It was not until about 12,000 years ago that humans began domesticating plants and animals. Bioarchaeologically and biochemically, this can be traced back to our earliest roots. Modern living conditions and the quality of human life are better today than ever before. However, neither physically nor psychosocially have we made this adjustment and we are paying a high health price for it. The studies presented allow us to reconstruct food supply, lifestyles, and dietary habits: from the earliest primates, through hunter-gatherers of the Paleolithic, farming communities since the beginning of the Anthropocene, to the Industrial Age and the present. The comprehensive data pool allows extraction of all findings of medical relevance. Our recent lifestyle and diet are essentially determined by our culture rather than by our millions of years of ancestry. Culture is permanently in a dominant position compared to natural evolution. Thereby culture does not form a contrast to nature but represents its result. There is no doubt that we are biologically adapted to culture, but it is questionable how much culture humans can cope with.
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Affiliation(s)
- Kurt W. Alt
- Center of Natural and Cultural Human History, Danube Private University, 3500 Krems, Austria
- Integrative Prehistory and Archaeological Science, University of Basel, 4055 Basel, Switzerland
- Correspondence:
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, 71906 Freiburg, Germany
| | - Johan Peter Woelber
- Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, 71906 Freiburg, Germany
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Gildner TE, Cepon-Robins TJ, Urlacher SS. Cumulative host energetic costs of soil-transmitted helminth infection. Trends Parasitol 2022; 38:629-641. [DOI: 10.1016/j.pt.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022]
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Cui Z, Holmes AJ, Zhang W, Hu D, Shao Q, Wang Z, Lu J, Raubenheimer D. Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items. Integr Zool 2021; 17:1147-1161. [PMID: 34767280 DOI: 10.1111/1749-4877.12601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Food supply is one of the major drivers of animal behavior, and the gut microbiome is an important mediator between food supply and its effects on physiology. However, predicting the outcome of diet change on microbiome and consequences for the animal has proven extremely challenging. We propose this reflects processes occurring at different scales. Inadequate accounting for the multi-level complexity of nutrition (nutrients, foods, diets) obscures the diet influence on microbiome and subsequently animal. Here, we present a detailed year-round, multi-level analysis of diet and microbiome changes in a wild population of a temperate primate, the rhesus macaque (Macaca mulatta). Total daily food and nutrient intake of 6 male and 6 female macaques was monitored in each of the 4 seasons (total 120 days observations). For each individual, we found significant variation in the microbiome between all 4 seasons. This response was more strongly correlated with changes in macronutrient intake than with food items and much of the response could be explained at the level of 6 ecological guilds-sets of taxa sharing similar responses to nutrient intake. We conclude that study of diet, microbiome, and animal performance in ecology will more effectively identify patterns if diet is recorded at the level of nutrient intake. Although microbiome response to diet does show variation in species-level taxa in response to food items, there is greater commonality in response at the level of guilds. A goal for microbiome researchers should be to identify genes encoding microbial attributes that can define such guilds.
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Affiliation(s)
- Zhenwei Cui
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Andrew J Holmes
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Wenjuan Zhang
- School of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Dalong Hu
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Qi Shao
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - Zhenlong Wang
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - Jiqi Lu
- School of Life Sciences, Institute of Biodiversity and Ecology, Zhengzhou University, Zhengzhou, China
| | - David Raubenheimer
- Centre for Nutritional Ecology, Centre for Sport Nutrition and Health, Zhengzhou University, Zhengzhou, China.,Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Alterations of the gut mycobiome in patients with MS. EBioMedicine 2021; 71:103557. [PMID: 34455391 PMCID: PMC8399064 DOI: 10.1016/j.ebiom.2021.103557] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/21/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in MS has not been studied. METHODS In this case-control observational study, we performed ITS sequencing and characterised the gut mycobiome in people with MS (pwMS) and healthy controls at baseline and after six months. FINDINGS The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Saccharomyces and Aspergillus were over-represented in pwMS. Saccharomyces was positively correlated with circulating basophils and negatively correlated with regulatory B cells, while Aspergillus was positively correlated with activated CD16+ dendritic cells in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial microbiome and immune cell subsets in the blood. Initial treatment with dimethyl fumarate, a common immunomodulatory therapy which also has fungicidal activity, did not cause uniform gut mycobiome changes across all pwMS. INTERPRETATION There is an alteration of the gut mycobiome in pwMS, compared to healthy controls. Further study is required to assess any causal association of the mycobiome with MS and its direct or indirect interactions with bacteria and autoimmunity. FUNDING This work was supported by the Washington University in St. Louis Institute of Clinical and Translational Sciences, funded, in part, by Grant Number # UL1 TR000448 from the National Institutes of Health, National Center for Advancing Translational Sciences, Clinical and Translational Sciences Award (Zhou Y, Piccio, L, Lovett-Racke A and Tarr PI); R01 NS102633-04 (Zhou Y, Piccio L); the Leon and Harriet Felman Fund for Human MS Research (Piccio L and Cross AH). Cantoni C. was supported by the National MS Society Career Transition Fellowship (TA-1805-31003) and by donations from Whitelaw Terry, Jr. / Valerie Terry Fund. Ghezzi L. was supported by the Italian Multiple Sclerosis Society research fellowship (FISM 2018/B/1) and the National Multiple Sclerosis Society Post-Doctoral Fellowship (FG- 1907-34474). Anne Cross was supported by The Manny & Rosalyn Rosenthal-Dr. John L. Trotter MS Center Chair in Neuroimmunology of the Barnes-Jewish Hospital Foundation. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
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Mallott EK, Amato KR. Host specificity of the gut microbiome. Nat Rev Microbiol 2021; 19:639-653. [PMID: 34045709 DOI: 10.1038/s41579-021-00562-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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12
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Campbell MC, Ranciaro A. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet 2021; 30:R98-R109. [PMID: 33847744 DOI: 10.1093/hmg/ddab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.
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Affiliation(s)
- Michael C Campbell
- Department of Biology, Howard University, EE Just Hall Biology Building, 415 College Street NW, Washington, DC 20059, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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13
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Locally adapted gut microbiomes mediate host stress tolerance. ISME JOURNAL 2021; 15:2401-2414. [PMID: 33658622 PMCID: PMC8319338 DOI: 10.1038/s41396-021-00940-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/29/2021] [Accepted: 02/11/2021] [Indexed: 01/04/2023]
Abstract
While evidence for the role of the microbiome in shaping host stress tolerance is becoming well-established, to what extent this depends on the interaction between the host and its local microbiome is less clear. Therefore, we investigated whether locally adapted gut microbiomes affect host stress tolerance. In the water flea Daphnia magna, we studied if the host performs better when receiving a microbiome from their source region than from another region when facing a stressful condition, more in particular exposure to the toxic cyanobacteria Microcystis aeruginosa. Therefore, a reciprocal transplant experiment was performed in which recipient, germ-free D. magna, isolated from different ponds, received a donor microbiome from sympatric or allopatric D. magna that were pre-exposed to toxic cyanobacteria or not. We tested for effects on host life history traits and gut microbiome composition. Our data indicate that Daphnia interact with particular microbial strains mediating local adaptation in host stress tolerance. Most recipient D. magna individuals performed better when inoculated with sympatric than with allopatric microbiomes. This effect was most pronounced when the donors were pre-exposed to the toxic cyanobacteria, but this effect was also pond and genotype dependent. We discuss how this host fitness benefit is associated with microbiome diversity patterns.
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14
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Amato KR, Chaves ÓM, Mallott EK, Eppley TM, Abreu F, Baden AL, Barnett AA, Bicca-Marques JC, Boyle SA, Campbell CJ, Chapman CA, De la Fuente MF, Fan P, Fashing PJ, Felton A, Fruth B, Fortes VB, Grueter CC, Hohmann G, Irwin M, Matthews JK, Mekonnen A, Melin AD, Morgan DB, Ostner J, Nguyen N, Piel AK, Pinacho-Guendulain B, Quintino-Arêdes EP, Razanaparany PT, Schiel N, Sanz CM, Schülke O, Shanee S, Souto A, Souza-Alves JP, Stewart F, Stewart KM, Stone A, Sun B, Tecot S, Valenta K, Vogel ER, Wich S, Zeng Y. Fermented food consumption in wild nonhuman primates and its ecological drivers. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:513-530. [PMID: 33650680 DOI: 10.1002/ajpa.24257] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Although fermented food use is ubiquitous in humans, the ecological and evolutionary factors contributing to its emergence are unclear. Here we investigated the ecological contexts surrounding the consumption of fruits in the late stages of fermentation by wild primates to provide insight into its adaptive function. We hypothesized that climate, socioecological traits, and habitat patch size would influence the occurrence of this behavior due to effects on the environmental prevalence of late-stage fermented foods, the ability of primates to detect them, and potential nutritional benefits. MATERIALS AND METHODS We compiled data from field studies lasting at least 9 months to describe the contexts in which primates were observed consuming fruits in the late stages of fermentation. Using generalized linear mixed-effects models, we assessed the effects of 18 predictor variables on the occurrence of fermented food use in primates. RESULTS Late-stage fermented foods were consumed by a wide taxonomic breadth of primates. However, they generally made up 0.01%-3% of the annual diet and were limited to a subset of fruit species, many of which are reported to have mechanical and chemical defenses against herbivores when not fermented. Additionally, late-stage fermented food consumption was best predicted by climate and habitat patch size. It was more likely to occur in larger habitat patches with lower annual mean rainfall and higher annual mean maximum temperatures. DISCUSSION We posit that primates capitalize on the natural fermentation of some fruits as part of a nutritional strategy to maximize periods of fruit exploitation and/or access a wider range of plant species. We speculate that these factors contributed to the evolutionary emergence of the human propensity for fermented foods.
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Affiliation(s)
- Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Óscar M Chaves
- Escuela de Biología, Universidad de Costa Rica, UCR, San José, Costa Rica
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Timothy M Eppley
- Institute for Conservation Research, San Diego Zoo Global, San Diego, California, USA.,Department of Anthropology, Portland State University, Portland, Oregon, USA
| | - Filipa Abreu
- Department of Biology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | - Andrea L Baden
- Department of Anthropology, Hunter College of the City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), City University of New York, New York, New York, USA
| | - Adrian A Barnett
- Amazon Mammals Research Group, National Amazon Research Institute (INPA), Manaus, AM, Brazil & Department of. Zoology, Federal University of Pernambuco, Recife, Prince Edward Island, Brazil
| | - Julio Cesar Bicca-Marques
- Laboratório de Primatologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, RS, Brazil
| | - Sarah A Boyle
- Department of Biology, Rhodes College, Memphis, Tennessee, USA
| | - Christina J Campbell
- Department of Anthropology, California State University Northridge, Northridge, California, USA
| | - Colin A Chapman
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, District of Columbia, USA.,School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa.,Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
| | | | - Pengfei Fan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Peter J Fashing
- Department of Anthropology and Environmental Studies Program, California State University Fullerton, Fullerton, California, USA.,Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Annika Felton
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences (SLU), Alnarp, Sweden
| | - Barbara Fruth
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Vanessa B Fortes
- Laboratório de Primatologia, Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Palmeira das Missões, RS, Brazil
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Gottfried Hohmann
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mitchell Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, Illinois, USA
| | - Jaya K Matthews
- Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, Australia.,Africa Research & Engagement Centre, The University of Western Australia, Crawley, Western Australia, Australia
| | - Addisu Mekonnen
- Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - David B Morgan
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, USA
| | - Julia Ostner
- Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Nga Nguyen
- Department of Anthropology and Environmental Studies Program, California State University Fullerton, Fullerton, California, USA.,Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Alex K Piel
- Department of Anthropology, University College London, London, United Kingdom
| | - Braulio Pinacho-Guendulain
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana (UAM), Lerma, Mexico.,Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional (CIIDIR), Unidad Oaxaca, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Erika Patricia Quintino-Arêdes
- Laboratório de Primatologia, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, RS, Brazil
| | - Patrick Tojotanjona Razanaparany
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, Japan.,Department of Zoology and Animal Biodiversity, University of Antananarivo, Antananarivo, Madagascar
| | - Nicola Schiel
- Department of Biology, Federal Rural University of Pernambuco, Recife, Pernambuco, Brazil
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri, USA.,Congo Program, Wildlife Conservation Society, Brazzaville, Congo
| | - Oliver Schülke
- Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Sam Shanee
- Neotropical Primate Conservation, Cornwall, United Kingdom
| | - Antonio Souto
- Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - João Pedro Souza-Alves
- Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Fiona Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Kathrine M Stewart
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Anita Stone
- Biology Department, California Lutheran University, Thousand Oaks, California, USA
| | - Binghua Sun
- School of Resource and Environmental Engineering, Anhui University, Hefei, China
| | - Stacey Tecot
- School of Anthropology, University of Arizona, Tucson, Arizona, USA
| | - Kim Valenta
- Department of Anthropology, University of Florida, Gainesville, Florida, USA
| | - Erin R Vogel
- Department of Anthropology, Rutgers University, New Brunswick, New Jersey, USA
| | - Serge Wich
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
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15
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Abstract
As human populations spread across the world, they adapted genetically to local conditions. So too did the resident microorganism communities that everyone carries with them. However, the collective influence of the diverse and dynamic community of resident microbes on host evolution is poorly understood. The taxonomic composition of the microbiota varies among individuals and displays a range of sometimes redundant functions that modify the physicochemical environment of the host and may alter selection pressures. Here we review known human traits and genes for which the microbiota may have contributed or responded to changes in host diet, climate, or pathogen exposure. Integrating host–microbiota interactions in human adaptation could offer new approaches to improve our understanding of human health and evolution.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
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16
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Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190598. [PMID: 32772669 PMCID: PMC7435160 DOI: 10.1098/rstb.2019.0598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2020] [Indexed: 12/23/2022] Open
Abstract
Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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17
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Egan S, Fukatsu T, Francino MP. Opportunities and Challenges to Microbial Symbiosis Research in the Microbiome Era. Front Microbiol 2020; 11:1150. [PMID: 32612581 PMCID: PMC7308722 DOI: 10.3389/fmicb.2020.01150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/06/2020] [Indexed: 01/04/2023] Open
Affiliation(s)
- Suhelen Egan
- Centre for Marine Science and Innovation (CMSI), School of Biological, Earth and Environmental Sciences (BEES), UNSW Sydney, Sydney, NSW, Australia
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Pilar Francino
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitária i Biomèdica de la Comunitat Valenciana (FISABIO)/Institut de Biologia Integrativa de Sistemes (Universitat de València i Consejo Superior de Investigaciones Científicas), València, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
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18
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Dunn RR, Amato KR, Archie EA, Arandjelovic M, Crittenden AN, Nichols LM. The Internal, External and Extended Microbiomes of Hominins. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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