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Barone M, Turroni S, Rampelli S, Soverini M, D’Amico F, Biagi E, Brigidi P, Troiani E, Candela M. Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context. PLoS One 2019; 14:e0220619. [PMID: 31393934 PMCID: PMC6687155 DOI: 10.1371/journal.pone.0220619] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more “ancestral” configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods–albeit with the exclusion of grains and pulses–along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.
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Affiliation(s)
- Monica Barone
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- * E-mail:
| | - Simone Rampelli
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Matteo Soverini
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Federica D’Amico
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Elena Biagi
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Emidio Troiani
- Primary Care Unit and Territorial Health, Social Security Institute, Cailungo, Republic of San Marino
| | - Marco Candela
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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52
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Schoilew K, Ueffing H, Dalpke A, Wolff B, Frese C, Wolff D, Boutin S. Bacterial biofilm composition in healthy subjects with and without caries experience. J Oral Microbiol 2019; 11:1633194. [PMID: 31275531 PMCID: PMC6598481 DOI: 10.1080/20002297.2019.1633194] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 01/03/2023] Open
Abstract
Objective:The composition of the oral microbiome differs distinctively between subjects with and without active caries. Still, caries research has mainly been focused on states of disease; aspects about how biofilm composition and structure maintain oral health still remain widely unclear. Therefore, the aim of the study was to compare the healthy oral microbiome of caries-free adult subjects with and without former caries experience using next generation sequencing methods. Methods: 46 samples were collected from subjects without any signs of untreated active caries. Samples of pooled supragingival plaque from 19 subjects without caries experience (NH; DMFT = 0) and 27 subjects with 'caries experience' ( CE; DMFT > 0 [F(T)> 0; D(T)= 0]) were analyzed by 16S ribosomal RNA amplicon sequencing. Results: Subjects with caries experience did not exhibit a dramatically modified supragingival plaque microbiome. However, we observed a slight and significant modification between the two groups, validated by PERMANOVA ( NH vs. CE: R2 0.04; p= 0.039). The composition of the microbiome of subjects with caries experience indicates a tendency to lower α-diversity and richness. Subjects without caries experience showed a significant higher evenness compared to patients with previous caries. LDA effect size (LEfSe) analysis demonstrated that the genus Haemophilus is significantly more frequent in patients with caries experience. For the group without caries experience LefSe analysis showed a set of 11 genera being significantly more frequent, including Corynebacterium, Fusobacterium, Capnocytophaga, Porphyromonas, Prevotella,and Leptotrichia. Conclusion: The analysis of the oral microbiome of subjects with and without caries experience indicates specific differences. With the presence of Corynebacterium and Fusobacterium subjects without caries experience exhibited more frequently organisms that are considered to be main actors in structural plaque formation and integration. The abundance of Corynebacterium might be interpreted as a signature for dental health.
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Affiliation(s)
- Kyrill Schoilew
- Department of Conservative Dentistry, School of Dental Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Helena Ueffing
- Department of Conservative Dentistry, School of Dental Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Institute of Medical Microbiology and Hygiene, Technical University Dresden, Dresden, Germany
| | - Björn Wolff
- Department of Conservative Dentistry, School of Dental Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Cornelia Frese
- Department of Conservative Dentistry, School of Dental Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Diana Wolff
- Department of Conservative Dentistry and Periodontology, Center of Dentistry, Oral Medicine and Maxillofacial Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
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53
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Optimal Microbiome Networks: Macroecology and Criticality. ENTROPY 2019; 21:e21050506. [PMID: 33267220 PMCID: PMC7514995 DOI: 10.3390/e21050506] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/04/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
The human microbiome is an extremely complex ecosystem considering the number of bacterial species, their interactions, and its variability over space and time. Here, we untangle the complexity of the human microbiome for the Irritable Bowel Syndrome (IBS) that is the most prevalent functional gastrointestinal disorder in human populations. Based on a novel information theoretic network inference model, we detected potential species interaction networks that are functionally and structurally different for healthy and unhealthy individuals. Healthy networks are characterized by a neutral symmetrical pattern of species interactions and scale-free topology versus random unhealthy networks. We detected an inverse scaling relationship between species total outgoing information flow, meaningful of node interactivity, and relative species abundance (RSA). The top ten interacting species are also the least relatively abundant for the healthy microbiome and the most detrimental. These findings support the idea about the diminishing role of network hubs and how these should be defined considering the total outgoing information flow rather than the node degree. Macroecologically, the healthy microbiome is characterized by the highest Pareto total species diversity growth rate, the lowest species turnover, and the smallest variability of RSA for all species. This result challenges current views that posit a universal association between healthy states and the highest absolute species diversity in ecosystems. Additionally, we show how the transitory microbiome is unstable and microbiome criticality is not necessarily at the phase transition between healthy and unhealthy states. We stress the importance of considering portfolios of interacting pairs versus single node dynamics when characterizing the microbiome and of ranking these pairs in terms of their interactions (i.e., species collective behavior) that shape transition from healthy to unhealthy states. The macroecological characterization of the microbiome is useful for public health and disease diagnosis and etiognosis, while species-specific analyses can detect beneficial species leading to personalized design of pre- and probiotic treatments and microbiome engineering.
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Sasaki K, Inoue J, Sasaki D, Hoshi N, Shirai T, Fukuda I, Azuma T, Kondo A, Osawa R. Construction of a Model Culture System of Human Colonic Microbiota to Detect Decreased Lachnospiraceae Abundance and Butyrogenesis in the Feces of Ulcerative Colitis Patients. Biotechnol J 2019; 14:e1800555. [PMID: 30791234 DOI: 10.1002/biot.201800555] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/28/2018] [Indexed: 01/27/2023]
Abstract
Compositional alteration of the gut microbiota is associated with ulcerative colitis (UC). Here, a model culture system is established for the in vitro human colonic microbiota of UC, which will be helpful for determining medical interventions. 16S ribosomal RNA sequencing confirms that UC models are successfully developed from fecal inoculum and retain the bacterial species biodiversity of UC feces. The UC models closely reproduce the microbial components and successfully preserve distinct clusters from the healthy subjects (HS), as observed in the feces. The relative abundance of bacteria belonging to the family Lachnospiraceae significantly decreases in the UC models compared to that in HS, as observed in the feces. The system detects significantly lower butyrogenesis in the UC models than that in HS, correlating with the decreased abundance of Lachnospiraceae. Interestingly, the relative abundance of Lachnospiraceae does not correlate with disease activity (defined as partial Mayo score), suggesting that Lachnospiraceae persists in UC patients at a decreased level, irrespective of the alteration in disease activity. Moreover, the system shows that administration of Clostridium butyricum MIYAIRI restores butyrogenesis in the UC model. Hence, the model detects deregulation in the intestinal environment in UC patients and may be useful for simulating the effect of probiotics.
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Affiliation(s)
- Kengo Sasaki
- Graduate School of Science, Technology and Innovation Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Jun Inoue
- Department of Internal Medicine, Division of Gastroenterology, Graduate School of Medicine, Kobe University, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Daisuke Sasaki
- Graduate School of Science, Technology and Innovation Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Namiko Hoshi
- Department of Internal Medicine, Division of Gastroenterology, Graduate School of Medicine, Kobe University, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Tomokazu Shirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Itsuko Fukuda
- Graduate School of Science, Technology and Innovation Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
| | - Takeshi Azuma
- Department of Internal Medicine, Division of Gastroenterology, Graduate School of Medicine, Kobe University, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ro Osawa
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan.,Research Center for Food Safety and Security, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo, 657-8501, Japan
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Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A, Urman B. The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls. Sci Rep 2019; 9:2204. [PMID: 30778155 PMCID: PMC6379373 DOI: 10.1038/s41598-019-39700-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Dysbiosis in the genital tract or gut microbiome can be associated with endometriosis. We sampled vaginal, cervical and gut microbiota from 14 women with histology proven stage 3/4 endometriosis and 14 healthy controls. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Despite overall similar vaginal, cervical and intestinal microbiota composition between stage 3/4 endometriosis group and controls, we observed differences at genus level. The complete absence of Atopobium in the vaginal and cervical microbiota of the stage 3/4 endometriosis group was noteworthy. In the cervical microbiota, Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma, all of which contain potentially pathogenic species, were increased in stage 3/4 endometriosis. More women in the stage 3/4 endometriosis group had Shigella/Escherichia dominant stool microbiome. Further studies can clarify whether the association is causal, and whether dysbiosis leads to endometriosis or endometriosis leads to dysbiosis.
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Affiliation(s)
- Baris Ata
- Department of Obstetrics and Gynecology, Koc University Faculty of Medicine, Istanbul, Turkey.
| | - Sule Yildiz
- Department of Obstetrics and Gynecology, Koc University Hospital, Istanbul, Turkey
| | - Engin Turkgeldi
- Department of Obstetrics and Gynecology, Koc University Hospital, Istanbul, Turkey
| | - Vicente Pérez Brocal
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
| | - Ener Cagri Dinleyici
- Eskisehir Osmangazi University Faculty of Medicine, Department of Pediatrics, Eskisehir, Turkey
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Institute for Integrative Systems Biology, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Bulent Urman
- Department of Obstetrics and Gynecology, Koc University Faculty of Medicine, Istanbul, Turkey
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56
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Henson MA, Phalak P. Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota. PLoS Comput Biol 2018; 14:e1006558. [PMID: 30376571 PMCID: PMC6226200 DOI: 10.1371/journal.pcbi.1006558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/09/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota represent a highly complex ecosystem comprised of approximately 1000 species that forms a mutualistic relationship with the human host. A critical attribute of the microbiota is high species diversity, which provides system robustness through overlapping and redundant metabolic capabilities. The gradual loss of bacterial diversity has been associated with a broad array of gut pathologies and diseases including malnutrition, obesity, diabetes and inflammatory bowel disease. We formulated an in silico community model of the gut microbiota by combining genome-scale metabolic reconstructions of 28 representative species to explore the relationship between species diversity and community growth. While the individual species offered a broad range of metabolic capabilities, communities optimized for maximal growth on simulated Western and high-fiber diets had low diversities and imbalances in short-chain fatty acid (SCFA) synthesis characterized by acetate overproduction. Community flux variability analysis performed with the 28-species model and a reduced 20-species model suggested that enhanced species diversity and more balanced SCFA production were achievable at suboptimal growth rates. We developed a simple method for constraining species abundances to sample the growth-diversity tradeoff and used the 20-species model to show that tradeoff curves for Western and high-fiber diets resembled Pareto-optimal surfaces. Compared to maximal growth solutions, suboptimal growth solutions were characterized by higher species diversity, more balanced SCFA synthesis and lower exchange rates of crossfed metabolites between more species. We hypothesized that modulation of crossfeeding relationships through host-microbiota interactions could be an important means for maintaining species diversity and suggest that community metabolic modeling approaches that allow multiobjective optimization of growth and diversity are needed for more realistic simulation of complex communities.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts, USA
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
- * E-mail:
| | - Poonam Phalak
- Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts, USA
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, USA
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57
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Kuo PH, Chung YCE. Moody microbiome: Challenges and chances. J Formos Med Assoc 2018; 118 Suppl 1:S42-S54. [PMID: 30262220 DOI: 10.1016/j.jfma.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 01/01/2023] Open
Abstract
Growing evidence link gut microbiome to the development and maturation of the central nervous system, which are regulated by microbiota potentially through stress response, neurotransmitter, neuroimmune, and endocrine pathways. The dysfunction of such microbiota-gut-brain axis is implicated in neuropsychiatric disorders, depression, and other stress-related conditions. Using affective disorders as our primary outcomes, we inspect the current evidence of microbiota studies mainly in human clinical samples. Additionally, to restore microbiome equilibrium in bacteria diversity and abundance might represent a novel strategy to prevent or treat mood symptoms. We reviewed findings from clinical trials regarding efficacy of probiotics supplement with or without antidepressant treatment, and adjuvant antimicrobiotics treatment. In microbiota studies, the considerations of host-microbiota interaction and bacteria-bacteria interaction are discussed. In conclusion, the roles of microbiota in depression and mania state are not fully elucidated. One of the challenges is to find reliable targets for functional analyses and experiments. Notwithstanding some inconsistencies and methodological limitations across studies, results from recent clinical trials support for the beneficial effects of probiotics on alleviating depressive symptoms and increasing well-beings. Moreover, modifying the composition of gut microbiota via antibiotics can be a viable adjuvant treatment option for individuals with depressive symptoms.
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Affiliation(s)
- Po-Hsiu Kuo
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.
| | - Yu-Chu Ella Chung
- Department of Public Health & Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
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58
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So D, Whelan K, Rossi M, Morrison M, Holtmann G, Kelly JT, Shanahan ER, Staudacher HM, Campbell KL. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. Am J Clin Nutr 2018; 107:965-983. [PMID: 29757343 DOI: 10.1093/ajcn/nqy041] [Citation(s) in RCA: 367] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/14/2018] [Indexed: 12/17/2022] Open
Abstract
Background Dysfunction of the gut microbiota is frequently reported as a manifestation of chronic diseases, and therefore presents as a modifiable risk factor in their development. Diet is a major regulator of the gut microbiota, and certain types of dietary fiber may modify bacterial numbers and metabolism, including short-chain fatty acid (SCFA) generation. Objective A systematic review and meta-analysis were undertaken to assess the effect of dietary fiber interventions on gut microbiota composition in healthy adults. Design A systematic search was conducted across MEDLINE, EMBASE, CENTRAL, and CINAHL for randomized controlled trials using culture and/or molecular microbiological techniques evaluating the effect of fiber intervention on gut microbiota composition in healthy adults. Meta-analyses via a random-effects model were performed on alpha diversity, prespecified bacterial abundances including Bifidobacterium and Lactobacillus spp., and fecal SCFA concentrations comparing dietary fiber interventions with placebo/low-fiber comparators. Results A total of 64 studies involving 2099 participants were included. Dietary fiber intervention resulted in higher abundance of Bifidobacterium spp. (standardized mean difference (SMD): 0.64; 95% CI: 0.42, 0.86; P < 0.00001) and Lactobacillus spp. (SMD: 0.22; 0.03, 0.41; P = 0.02) as well as fecal butyrate concentration (SMD: 0.24; 0.00, 0.47; P = 0.05) compared with placebo/low-fiber comparators. Subgroup analysis revealed that fructans and galacto-oligosaccharides led to significantly greater abundance of both Bifidobacterium spp. and Lactobacillus spp. compared with comparators (P < 0.00001 and P = 0.002, respectively). No differences in effect were found between fiber intervention and comparators for α-diversity, abundances of other prespecified bacteria, or other SCFA concentrations. Conclusions Dietary fiber intervention, particularly involving fructans and galacto-oligosaccharides, leads to higher fecal abundance of Bifidobacterium and Lactobacillus spp. but does not affect α-diversity. Further research is required to better understand the role of individual fiber types on the growth of microbes and the overall gut microbial community. This review was registered at PROSPERO as CRD42016053101.
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Affiliation(s)
- Daniel So
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia
| | - Kevin Whelan
- Department of Nutritional Sciences, King's College, London, United Kingdom
| | - Megan Rossi
- Department of Nutritional Sciences, King's College, London, United Kingdom
| | - Mark Morrison
- The University of Queensland Diamantina Institute, Translational Research Institute.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Gerald Holtmann
- Faculty of Medicine, University of Queensland, Brisbane, Australia.,Department of Gastroenterology & Hepatology
| | - Jaimon T Kelly
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia
| | - Erin R Shanahan
- The University of Queensland Diamantina Institute, Translational Research Institute.,Department of Gastroenterology & Hepatology
| | | | - Katrina L Campbell
- Faculty of Health Sciences and Medicine, Bond University, Gold Coast, Australia.,Department of Nutrition and Dietetics, Princess Alexandra Hospital, Brisbane, Australia
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Abstract
Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states. Although some questions have been raised about how this term is applied, its use continues undiminished in the literature. We investigate the ways in which microbiome researchers discuss dysbiosis and then assess the impact of different concepts of dysbiosis on microbiome research. After an overview of the term's historical roots, we conduct quantitative and qualitative analyses of a large selection of contemporary dysbiosis statements. We categorize both short definitions and longer conceptual statements about dysbiosis. Further analysis allows us to identify the problematic implications of how dysbiosis is used, particularly with regard to causal hypotheses and normal-abnormal distinctions. We suggest that researchers should reflect carefully on the ways in which they discuss dysbiosis, in order for the field to continue to develop greater predictive scope and explanatory depth.
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Affiliation(s)
- Katarzyna B Hooks
- Centre de Bioinformatique de Bordeaux, Centre de Génomique Fonctionnelle de Bordeaux, University of Bordeaux, Bordeaux, France
- Immunoconcept, CNRS UMR 5164, University of Bordeaux, Bordeaux, France
| | - Maureen A O'Malley
- Centre de Bioinformatique de Bordeaux, Centre de Génomique Fonctionnelle de Bordeaux, University of Bordeaux, Bordeaux, France
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60
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Dietary and lifestyle disease indices and caecal microbiota in high fat diet, dietary fibre free diet, or DSS induced IBD models in ICR mice. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.06.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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