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G-Santoyo I, Ramírez-Carrillo E, Sanchez JD, López-Corona O. Potential long consequences from internal and external ecology: loss of gut microbiota antifragility in children from an industrialized population compared with an indigenous rural lifestyle. J Dev Orig Health Dis 2023; 14:469-480. [PMID: 37222148 DOI: 10.1017/s2040174423000144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Human health is strongly mediated by the gut microbiota ecosystem, which, in turn, depends not only on its state but also on its dynamics and how it responds to perturbations. Healthy microbiota ecosystems tend to be in criticality and antifragile dynamics corresponding to a maximum complexity configuration, which may be assessed with information and network theory analysis. Under this complex system perspective, we used a new analysis of published data to show that a children's population with an industrialized urban lifestyle from Mexico City exhibits informational and network characteristics similar to parasitized children from a rural indigenous population in the remote mountainous region of Guerrero, México. We propose then, that in this critical age for gut microbiota maturation, the industrialized urban lifestyle could be thought of as an external perturbation to the gut microbiota ecosystem, and we show that it produces a similar loss in criticality/antifragility as the one observed by internal perturbation due to parasitosis by the helminth A. lumbricoides. Finally, several general complexity-based guidelines to prevent or restore gut ecosystem antifragility are discussed.
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Affiliation(s)
- Isaac G-Santoyo
- Neuroecology Lab, Department of Psychology, UNAM, México, 04510
- Unidad de Investigación en Psicobiología y Neurociencias, Department of Psychology, UNAM, México, 04510
| | | | | | - Oliver López-Corona
- Investigadores por México (IxM)-CONACyT, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas (IIMAS), UNAM, México, 04510
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D'Aloisio LD, Shetty V, Ballal M, Gibson DL. Following the Indian Immigrant: adoption of westernization results in a western gut microbiome and an increased risk of inflammatory bowel diseases. FEMS Microbiol Ecol 2022; 98:6825449. [PMID: 36370451 DOI: 10.1093/femsec/fiac133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/01/2022] [Accepted: 11/10/2022] [Indexed: 11/13/2022] Open
Abstract
Indians who migrate to westernized countries such as Canada, the USA, and the UK are at an increased risk of developing inflammatory bowel disease (IBD). While the underlying aetiology of IBD remains unclear, a gut microbiome, i.e. no longer symbiotic with its host, is a major player. Increasing IBD incidence in Indian immigrants may be due to the adoption of western practices that result in loss of tolerance of a symbiotic community in the gut and its underlying immune responses. However, little is known about the microbial changes in the Indian gut, including shifts in the microbiome when they migrate to westernized countries. In this Current Opinion, we discuss what is known about the Indian gut microbiome and how living in a westernized environment may be impeding what was once a symbiotic relationship with their gut microbiome and intestinal mucosae, which may be the driving factor in their increased risk of IBD.
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Affiliation(s)
- Leah D D'Aloisio
- Department of Biology, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada
| | - Vignesh Shetty
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, 576104 Manipal, India.,Department of Medicine, University of Cambridge, CB2 2QQ Cambridge, United Kingdom
| | - Mamatha Ballal
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, 576104 Manipal, India
| | - Deanna L Gibson
- Department of Biology, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada.,Department of Medicine, University of British Columbia- Okanagan Campus, V1V 1V7 Kelowna, Canada
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Sánchez-Quinto A, Cerqueda-García D, Falcón LI, Gaona O, Martínez-Correa S, Nieto J, G-Santoyo I. Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. Microorganisms 2020; 8:E1592. [PMID: 33081076 DOI: 10.3390/microorganisms8101592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.
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Anani H, Zgheib R, Hasni I, Raoult D, Fournier PE. Interest of bacterial pangenome analyses in clinical microbiology. Microb Pathog 2020; 149:104275. [PMID: 32562810 DOI: 10.1016/j.micpath.2020.104275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.
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Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Issam Hasni
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
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Schnorr SL. Meanings, measurements, and musings on the significance of patterns in human microbiome variation. Curr Opin Genet Dev 2018; 53:43-52. [DOI: 10.1016/j.gde.2018.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 01/23/2023]
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Skelly E, Kapellas K, Cooper A, Weyrich LS. Consequences of colonialism: A microbial perspective to contemporary Indigenous health. Am J Phys Anthropol 2018; 167:423-437. [DOI: 10.1002/ajpa.23637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Emily Skelly
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Kostas Kapellas
- Australian Research Centre for Population Oral Health, Adelaide Dental School University of Adelaide Adelaide South Australia Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
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Abstract
Diet has shaped microbiota profiles through human evolution.
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Affiliation(s)
- T. Requena
- Department of Food Biotechnology and Microbiology
- Institute of Food Science Research
- 28049 Madrid
- Spain
| | - M. C. Martínez-Cuesta
- Department of Food Biotechnology and Microbiology
- Institute of Food Science Research
- 28049 Madrid
- Spain
| | - C. Peláez
- Department of Food Biotechnology and Microbiology
- Institute of Food Science Research
- 28049 Madrid
- Spain
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Abstract
Mammals harbor complex assemblages of gut bacteria that are deeply integrated with their hosts' digestive, immune, and neuroendocrine systems. Recent work has revealed that there has been a substantial loss of gut bacterial diversity from humans since the divergence of humans and chimpanzees. This bacterial depauperation began in humanity's ancient evolutionary past and has accelerated in recent years with the advent of modern lifestyles. Today, humans living in industrialized societies harbor the lowest levels of gut bacterial diversity of any primate for which metagenomic data are available, a condition that may increase risk of infections, autoimmune disorders, and metabolic syndrome. Some missing gut bacteria may remain within under-sampled human populations, whereas others may be globally extinct and unrecoverable.
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Affiliation(s)
- Andrew H Moeller
- Miller Institute for Basic Research in Science, University of California, Berkeley, 2538 Channing Way, Berkley, CA 94720, United States.
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