101
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Bahrami F, Haghighi A, Zamini G, Khadem-Erfan MB, Azargashb E. Prevalence and associated risk factors of intestinal parasitic infections in Kurdistan province, northwest Iran. COGENT MEDICINE 2018. [DOI: 10.1080/2331205x.2018.1503777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Fares Bahrami
- Zoonoses Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Haghighi
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghasem Zamini
- Department of Parasitology and Mycology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Mohammad Bagher Khadem-Erfan
- Department of Parasitology and Mycology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Cellular and Molecular Research Center, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Eznolla Azargashb
- Department of Community Medicine & Health, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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102
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Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P. Metagenomic analysis of gut microbial communities from a Central Asian population. BMJ Open 2018; 8:e021682. [PMID: 30056386 PMCID: PMC6067398 DOI: 10.1136/bmjopen-2018-021682] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Changes in the gut microbiota are increasingly recognised to be involved in many diseases. This ecosystem is known to be shaped by many factors, including climate, geography, host nutrition, lifestyle and medication. Thus, knowledge of varying populations with different habits is important for a better understanding of the microbiome. DESIGN We therefore conducted a metagenomic analysis of intestinal microbiota from Kazakh donors, recruiting 84 subjects, including male and female healthy subjects and metabolic syndrome (MetS) patients aged 25-75 years, from the Kazakh administrative centre, Astana. We characterise and describe these microbiomes, the first deep-sequencing cohort from Central Asia, in comparison with a global dataset (832 individuals from five countries on three continents), and explore correlations between microbiota, clinical and laboratory parameters as well as with nutritional data from Food Frequency Questionnaires. RESULTS We observe that Kazakh microbiomes are relatively different from both European and East Asian counterparts, though similar to other Central Asian microbiomes, with the most striking difference being significantly more samples falling within the Prevotella-rich enterotype, potentially reflecting regional diet and lifestyle. We show that this enterotype designation remains stable within an individual over time in 82% of cases. We further observe gut microbiome features that distinguish MetS patients from controls (eg, significantly reduced Firmicutes to Bacteroidetes ratio, Bifidobacteria and Subdoligranulum, alongside increased Prevotella), though these overlap little with previously published reports and thus may reflect idiosyncrasies of the present cohort. CONCLUSION Taken together, this exploratory study describes gut microbiome data from an understudied population, providing a starting point for further comparative work on biogeography and research on widespread diseases. TRIAL REGISTRATION NUMBER ISRCTN37346212; Post-results.
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Affiliation(s)
| | - Sofia K Forslund
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
- ECRC, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Experimental and Clinical Research Centre, a cooperation of Charité-Universitätsmedizin and the Max-Delbrück Centre, Berlin, Berlin, Germany
| | - Paul Igor Costea
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
| | | | | | - Maira Urazova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Talgat Nurgozhin
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Valery Benberin
- Medical Center under the Office of the Kazakh President, Astana, Kazakhstan
| | - Marja Driessen
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
| | - Rajna Hercog
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
| | - Anita Yvonne Voigt
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
| | - Vladimir Benes
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
| | - Stefanie Kandels-Lewis
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
| | - Shinichi Sunagawa
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Ivica Letunic
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
| | - Peer Bork
- The European Molecular Biology Laboratory (EMBL), Structural and Computational Biology, Heidelberg, Germany
- ECRC, Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
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103
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Mallott EK, Amato KR. The microbial reproductive ecology of white-faced capuchins (Cebus capucinus). Am J Primatol 2018; 80:e22896. [PMID: 29984842 DOI: 10.1002/ajp.22896] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/18/2018] [Accepted: 06/22/2018] [Indexed: 01/01/2023]
Abstract
Changes in reproductive status influence energy and nutrient requirements in female primates. The gut microbiota may buffer changes in energy demands, with shifts in community composition increasing the energy production potential of the gut during pregnancy and lactation. In this study, we examine changes in the gut microbiome of wild, female white-faced capuchins (Cebus capucinus) across different reproductive states. Fecal samples (n = 39) were collected from five adult females over the course of a year. Gut microbial community composition was assessed using 16S rRNA gene sequences, and PICRUSt was used to make metagenomic functional predictions. We found a significant relationship between reproductive state and both the structure and predicted function of the gut microbiome, neither of which were associated with host diet. For example, the relative abundance of Firmicutes was significantly lower in lactating females compared with cycling females; the relative abundance of Actinobacteria was significantly higher in pregnant females compared with lactating females, and there was a trend toward higher relative abundances of Proteobacteria in pregnant females compared with cycling females. The results of this study suggest that, in addition to behavioral and dietary adaptions, the gut microbiota may play a role in allowing female primates to meet their changing energetic needs during reproduction. Further studies of the "microbial reproductive ecology" of primates will help advance our understanding of gut microbial contributions to primate energetics.
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Affiliation(s)
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois
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104
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Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns. mSystems 2018; 3:mSystems00007-18. [PMID: 29963639 PMCID: PMC6020473 DOI: 10.1128/msystems.00007-18] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/02/2018] [Indexed: 12/25/2022] Open
Abstract
Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition. Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation. To explore this, we evaluated the fecal bacterial and eukaryotic microbiota in 156 asymptomatic adult subjects from a rural population in Xoxocotla, Mexico. Colonization with Blastocystis was strongly associated with an increase in bacterial alpha diversity and broad changes in beta diversity and with more discrete changes to the microbial eukaryome. More than 230 operational taxonomic units (OTUs), including those of dominant species Prevotella copri and Ruminococcus bromii, were differentially abundant in Blastocystis-colonized individuals. Large functional changes accompanied these observations, with differential abundances of 202 (out of 266) predicted metabolic pathways (PICRUSt), as well as lower fecal concentrations of acetate, butyrate, and propionate in colonized individuals. Fecal calprotectin was markedly decreased in association with Blastocystis colonization, suggesting that this ecological shift induces subclinical immune consequences to the asymptomatic host. This work is the first to show a direct association between the presence of Blastocystis and shifts in the gut bacterial and eukaryotic microbiome in the absence of gastrointestinal disease or inflammation. These results prompt further investigation of the role Blastocystis and other eukaryotes play within the human microbiome. IMPORTANCE Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition.
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105
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Vlčková K, Pafčo B, Petrželková KJ, Modrý D, Todd A, Yeoman CJ, Torralba M, Wilson BA, Stumpf RM, White BA, Nelson KE, Leigh SR, Gomez A. Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas. Front Microbiol 2018; 9:1202. [PMID: 29963018 PMCID: PMC6013710 DOI: 10.3389/fmicb.2018.01202] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Relationships between gastrointestinal parasites (GIPs) and the gastrointestinal microbiome (GIM) are widely discussed topics across mammalian species due to their possible impact on the host's health. GIPs may change the environment determining alterations in GIM composition. We evaluated the associations between GIP infections and fecal microbiome composition in two habituated and two unhabituated groups of wild western lowland gorillas (Gorilla g. gorilla) from Dzanga Sangha Protected Areas, Central African Republic. We examined 43 fecal samples for GIPs and quantified strongylid nematodes. We characterized fecal microbiome composition through 454 pyrosequencing of the V1-V3 region of the bacterial 16S rRNA gene. Entamoeba spp. infections were associated with significant differences in abundances of bacterial taxa that likely play important roles in nutrition and metabolism for the host, besides being characteristic members of the gorilla gut microbiome. We did not observe any relationships between relative abundances of several bacterial taxa and strongylid egg counts. Based on our findings, we suggest that there is a significant relationship between fecal microbiome and Entamoeba infection in wild gorillas. This study contributes to the overall knowledge about factors involved in modulating GIM communities in great apes.
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Affiliation(s)
- Klára Vlčková
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
| | - Barbora Pafčo
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia.,Liberec Zoo, Liberec, Czechia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - David Modrý
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia.,Central European Institute for Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czechia
| | - Angelique Todd
- WWF, Dzanga Sangha Protected Areas, Bangui, Central African Republic
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, United States
| | | | - Brenda A Wilson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rebecca M Stumpf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Bryan A White
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Karen E Nelson
- J. Craig Venter Institute, Rockville, MD, United States.,J. Craig Venter Institute, La Jolla, CA, United States
| | - Steven R Leigh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Anthropology, University of Colorado at Boulder, Boulder, CO, United States
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, St Paul, MN, United States
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106
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Cornick S, Chadee K. Entamoeba histolytica: Host parasite interactions at the colonic epithelium. Tissue Barriers 2018; 5:e1283386. [PMID: 28452682 DOI: 10.1080/21688370.2017.1283386] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Entamoeba histolytica (Eh) is the protozoan parasite responsible for intestinal amebiasis and interacts dynamically with the host intestinal epithelium during disease pathogenesis. A multifaceted pathogenesis profile accounts for why 90% of individuals infected with Eh are largely asymptomatic. For 100 millions individuals that are infected each year, key interactions within the intestinal mucosa dictate disease susceptibility. The ability for Eh to induce amebic colitis and disseminate into extraintestinal organs depends on the parasite competing with indigenous bacteria and overcoming the mucus barrier, binding to host cells inducing their cell death, invasion through the mucosa and outsmarting the immune system. In this review we summarize how Eh interacts with the intestinal epithelium and subverts host defense mechanisms in disease pathogenesis.
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Affiliation(s)
- Steve Cornick
- a Department of Microbiology, Immunology and Infectious Diseases , Snyder Institute for Chronic Diseases, University of Calgary , Calgary , Alberta , Canada
| | - Kris Chadee
- a Department of Microbiology, Immunology and Infectious Diseases , Snyder Institute for Chronic Diseases, University of Calgary , Calgary , Alberta , Canada
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107
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Leung JM, Graham AL, Knowles SCL. Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens. Front Microbiol 2018; 9:843. [PMID: 29867790 PMCID: PMC5960673 DOI: 10.3389/fmicb.2018.00843] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/12/2018] [Indexed: 12/14/2022] Open
Abstract
The vertebrate gut teems with a large, diverse, and dynamic bacterial community that has pervasive effects on gut physiology, metabolism, and immunity. Under natural conditions, these microbes share their habitat with a similarly dynamic community of eukaryotes (helminths, protozoa, and fungi), many of which are well-known parasites. Both parasites and the prokaryotic microbiota can dramatically alter the physical and immune landscape of the gut, creating ample opportunities for them to interact. Such interactions may critically alter infection outcomes and affect overall host health and disease. For instance, parasite infection can change how a host interacts with its bacterial flora, either driving or protecting against dysbiosis and inflammatory disease. Conversely, the microbiota can alter a parasite's colonization success, replication, and virulence, shifting it along the parasitism-mutualism spectrum. The mechanisms and consequences of these interactions are just starting to be elucidated in an emergent transdisciplinary area at the boundary of microbiology and parasitology. However, heterogeneity in experimental designs, host and parasite species, and a largely phenomenological and taxonomic approach to synthesizing the literature have meant that common themes across studies remain elusive. Here, we use an ecological perspective to review the literature on interactions between the prokaryotic microbiota and eukaryotic parasites in the vertebrate gut. Using knowledge about parasite biology and ecology, we discuss mechanisms by which they may interact with gut microbes, the consequences of such interactions for host health, and how understanding parasite-microbiota interactions may lead to novel approaches in disease control.
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Affiliation(s)
- Jacqueline M Leung
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
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108
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Associations between Gut Microbiota and Common Luminal Intestinal Parasites. Trends Parasitol 2018; 34:369-377. [DOI: 10.1016/j.pt.2018.02.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 02/08/2023]
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109
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Nishida AH, Ochman H. Rates of gut microbiome divergence in mammals. Mol Ecol 2018; 27:1884-1897. [PMID: 29290090 PMCID: PMC5935551 DOI: 10.1111/mec.14473] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/14/2017] [Accepted: 12/14/2017] [Indexed: 12/13/2022]
Abstract
The variation and taxonomic diversity among mammalian gut microbiomes raises several questions about the factors that contribute to the rates and patterns of change in these microbial communities. By comparing the microbiome compositions of 112 species representing 14 mammalian orders, we assessed how host and ecological factors contribute to microbiome diversification. Except in rare cases, the same bacterial phyla predominate in mammalian gut microbiomes, and there has been some convergence of microbiome compositions according to dietary category across all mammalians lineages except Chiropterans (bats), which possess high proportions of Proteobacteria and tend to be most similar to one another regardless of diet. At lower taxonomic ranks (families, genera, 97% OTUs), bacteria are more likely to be associated with a particular mammalian lineage than with a particular dietary category, resulting in a strong phylogenetic signal in the degree to which microbiomes diverge. Despite different physiologies, the gut microbiomes of several mammalian lineages have diverged at roughly the same rate over the past 75 million years; however, the gut microbiomes of Cetartiodactyla (ruminants, whales, hippopotami) have evolved much faster and those of Chiropterans much slower. Contrary to expectations, the number of dietary transitions within a lineage does not influence rates of microbiome divergence, but instead, some of the most dramatic changes are associated with the loss of bacterial taxa, such as those accompanying the transition from terrestrial to marine lifestyles and the evolution of hominids.
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Affiliation(s)
- Alex H Nishida
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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110
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Xiong J, Yu W, Dai W, Zhang J, Qiu Q, Ou C. Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota. Appl Microbiol Biotechnol 2018; 102:3315-3326. [PMID: 29497796 DOI: 10.1007/s00253-018-8874-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 02/04/2018] [Accepted: 02/12/2018] [Indexed: 10/17/2022]
Abstract
One common notion is emerging that gut eukaryotes are commensal or beneficial, rather than detrimental. To date, however, surprisingly few studies have been taken to discern the factors that govern the assembly of gut eukaryotes, despite growing interest in the dysbiosis of gut microbiota-disease relationship. Herein, we firstly explored how the gut eukaryotic microbiotas were assembled over shrimp postlarval to adult stages and a disease progression. The gut eukaryotic communities changed markedly as healthy shrimp aged, and converged toward an adult-microbiota configuration. However, the adult-like stability was distorted by disease exacerbation. A null model untangled that the deterministic processes that governed the gut eukaryotic assembly tended to be more important over healthy shrimp development, whereas this trend was inverted as the disease progressed. After ruling out the baseline of gut eukaryotes over shrimp ages, we identified disease-discriminatory taxa (species level afforded the highest accuracy of prediction) that characteristic of shrimp health status. The profiles of these taxa contributed an overall 92.4% accuracy in predicting shrimp health status. Notably, this model can accurately diagnose the onset of shrimp disease. Interspecies interaction analysis depicted how the disease-discriminatory taxa interacted with one another in sustaining shrimp health. Taken together, our findings offer novel insights into the underlying ecological processes that govern the assembly of gut eukaryotes over shrimp postlarval to adult stages and a disease progression. Intriguingly, the established model can quantitatively and accurately predict the incidences of shrimp disease.
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Affiliation(s)
- Jinbo Xiong
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China. .,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
| | - Weina Yu
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Wenfang Dai
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jinjie Zhang
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China
| | - Qiongfen Qiu
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China
| | - Changrong Ou
- Faculty of Marine Science, Ningbo University, Ningbo, 315211, China
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111
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Guan Y, Feng M, Min X, Zhou H, Fu Y, Tachibana H, Cheng X. Characteristics of inflammatory reactions during development of liver abscess in hamsters inoculated with Entamoeba nuttalli. PLoS Negl Trop Dis 2018; 12:e0006216. [PMID: 29420539 PMCID: PMC5821383 DOI: 10.1371/journal.pntd.0006216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/21/2018] [Accepted: 01/05/2018] [Indexed: 12/28/2022] Open
Abstract
Background Entamoeba nuttalli is an intestinal protozoan with pathogenic potential that can cause amebic liver abscess. It is highly prevalent in wild and captive macaques. Recently, cysts were detected in a caretaker of nonhuman primates in a zoo, indicating that E. nuttalli may be a zoonotic pathogen. Therefore, it is important to evaluate the pathogenicity of E. nuttalli in detail and in comparison with that of E. histolytica. Methodology/Principal findings Trophozoites of E. nuttalli GY4 and E. histolytica SAW755 strains were inoculated into liver of hamsters. Expression levels of proinflammatory factors of hamsters and virulence factors from E. histolytica and E. nuttalli were compared between the two parasites. Inoculations with trophozoites of E. nuttalli resulted in an average necrotic area of 24% in liver tissue in 7 days, whereas this area produced by E. histolytica was nearly 50%. Along with the mild liver tissue damage induced by E. nuttalli, expression levels of proinflammatory factors (TNF-α, IL-6 and IL-1β) and amebic virulence protein genes (lectins, cysteine proteases and amoeba pores) in local tissues were lower with E. nuttalli in comparison with E. histolytica. In addition, M2 type macrophages were increased in E. nuttalli-induced amebic liver abscesses in the late stage of disease progression and lysate of E. nuttalli trophozoites induced higher arginase expression than E. histolytica in vitro. Conclusions/Significance The results show that differential secretion of amebic virulence proteins during E. nuttalli infection triggered lower levels of secretion of various cytokines and had an impact on polarization of macrophages towards a M1/M2 balance. However, regardless of the degree of macrophage polarization, there is unambiguous evidence of an intense acute inflammatory reaction in liver of hamsters after infection by both Entamoeba species. Entamoeba nuttalli is the phylogenetically closest protozoan to Entamoeba histolytica and is highly prevalent in macaques. Previous studies have indicated that E. nuttalli is virulent in a hamster model. In this study, we compared the immunopathological basis of formation of liver abscess in hamsters between E. nuttalli and E. histolytica. Mild liver tissue damage developed after intrahepatic injection of trophozoites of E. nuttalli, and lower expression levels of genes for host proinflammatory factors and amebic virulence proteins were detected at the edges of liver abscesses induced by E. nuttalli. In addition, alternatively activated macrophages were increased in E. nuttalli-induced liver abscesses in the late stage of disease progression. The lysate of E. nuttalli trophozoites also induced higher arginase expression than E. histolytica in vitro. Polarization of macrophages is likely to affect the degree of acute inflammatory reactions in liver in an animal model during E. nuttalli infection. Our data reveal new characteristics of abscess formation by E. nuttalli.
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Affiliation(s)
- Yue Guan
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Meng Feng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiangyang Min
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Clinical Laboratory Medicine, Yangpu Hospital of Tongji University, Shanghai, China
| | - Hang Zhou
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yongfeng Fu
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hiroshi Tachibana
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- * E-mail: (XC); (HT)
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- * E-mail: (XC); (HT)
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112
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Requena T, Martínez-Cuesta MC, Peláez C. Diet and microbiota linked in health and disease. Food Funct 2018; 9:688-704. [DOI: 10.1039/c7fo01820g] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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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113
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Matheson K, Bombay A, Anisman H. Culture as an ingredient of personalized medicine. J Psychiatry Neurosci 2018; 43:3-6. [PMID: 29252161 PMCID: PMC5747533 DOI: 10.1503/jpn.170234] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
| | | | - Hymie Anisman
- Correspondence to: H. Anisman, Department of Neuroscience, Carleton University, Ottawa ON K1S 5B6;
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114
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Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 2017; 357:802-806. [PMID: 28839072 DOI: 10.1126/science.aan4834] [Citation(s) in RCA: 499] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022]
Abstract
Although humans have cospeciated with their gut-resident microbes, it is difficult to infer features of our ancestral microbiome. Here, we examine the microbiome profile of 350 stool samples collected longitudinally for more than a year from the Hadza hunter-gatherers of Tanzania. The data reveal annual cyclic reconfiguration of the microbiome, in which some taxa become undetectable only to reappear in a subsequent season. Comparison of the Hadza data set with data collected from 18 populations in 16 countries with varying lifestyles reveals that gut community membership corresponds to modernization: Notably, the taxa within the Hadza that are the most seasonally volatile similarly differentiate industrialized and traditional populations. These data indicate that some dynamic lineages of microbes have decreased in prevalence and abundance in modernized populations.
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Affiliation(s)
- Samuel A Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeff Leach
- Human Food Project, 53600 Highway 118, Terlingua, TX 79852, USA.,The Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, Lambeth Palace Road, London SE1 7EH, UK
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carlos G Gonzalez
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA
| | - Joshua S Lichtman
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA
| | - Gregor Reid
- Lawson Health Research Institute and Western University, London, Ontario N6A 4V2, Canada
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering and Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
| | | | | | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford School of Medicine, Stanford University, Stanford, CA 94025, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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115
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Partida-Rodríguez O, Serrano-Vázquez A, Nieves-Ramírez ME, Moran P, Rojas L, Portillo T, González E, Hernández E, Finlay BB, Ximenez C. Human Intestinal Microbiota: Interaction Between Parasites and the Host Immune Response. Arch Med Res 2017; 48:690-700. [PMID: 29290328 DOI: 10.1016/j.arcmed.2017.11.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023]
Abstract
The human gut is a highly complex ecosystem with an extensive microbial community, and the influence of the intestinal microbiota reaches the entire host organism. For example, the microbiome regulates fat storage, stimulates or renews epithelial cells, and influences the development and maturation of the brain and the immune system. Intestinal microbes can protect against infection by pathogenic bacteria, viruses, fungi and parasites. Hence, the maintenance of homeostasis between the gut microbiota and the rest of the body is crucial for health, with dysbiosis affecting disease. This review focuses on intestinal protozoa, especially those still representing a public health problem in Mexico, and their interactions with the microbiome and the host. The decrease in prevalence of intestinal helminthes in humans left a vacant ecological niche that was quickly occupied by protozoa. Although the mechanisms governing the interaction between intestinal microbiota and protozoa are poorly understood, it is known that the composition of the intestinal bacterial populations modulates the progression of protozoan infection and the outcome of parasitic disease. Most reports on the complex interactions between intestinal bacteria, protozoa and the immune system emphasize the protective role of the microbiota against protozoan infection. Insights into such protection may facilitate the manipulation of microbiota components to prevent and treat intestinal protozoan infections. Here we discuss recent findings about the immunoregulatory effect of intestinal microbiota with regards to intestinal colonization by protozoa, focusing on infections by Entamoeba histolytica, Blastocystis spp, Giardia duodenalis, Toxoplasma gondii and Cryptosporidium parvum. The possible consequences of the microbiota on parasitic, allergic and autoimmune disorders are also considered.
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Affiliation(s)
- Oswaldo Partida-Rodríguez
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México; Michael Smith Laboratories, University of Brithish Columbia, Vancouver, Canada
| | - Angélica Serrano-Vázquez
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Miriam E Nieves-Ramírez
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Patricia Moran
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Liliana Rojas
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Tobias Portillo
- Unidad de Bioinformática, Bioestadística y Biología Computacional. Red de Apoyo a la Investigación Científica, Universidad Nacional Autónoma de México, Instituto Nacional De Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
| | - Enrique González
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Eric Hernández
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - B Brett Finlay
- Michael Smith Laboratories, University of Brithish Columbia, Vancouver, Canada
| | - Cecilia Ximenez
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México.
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116
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Abstract
The trillions of microbes living in the gut—the gut microbiota—play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity’s near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations. Finally, we propose that this broader phylogenetic perspective is useful for understanding the mechanisms underlying human–microbiome interactions.
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Affiliation(s)
- Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. .,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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117
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Lassalle F, Spagnoletti M, Fumagalli M, Shaw L, Dyble M, Walker C, Thomas MG, Bamberg Migliano A, Balloux F. Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet. Mol Ecol 2017; 27:182-195. [PMID: 29165844 DOI: 10.1111/mec.14435] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/06/2017] [Indexed: 01/22/2023]
Abstract
Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high-coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter-gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter-gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease-mediated pH regulation as candidate adaptations of the microbiome to the hunter-gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.
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Affiliation(s)
- Florent Lassalle
- University College London, UCL Genetics Institute, London, UK.,Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | | | - Liam Shaw
- University College London, UCL Genetics Institute, London, UK
| | - Mark Dyble
- Department of Anthropology, University College London, London, UK.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Mark G Thomas
- University College London, UCL Genetics Institute, London, UK
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118
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Lee YY, Hassan SA, Ismail IH, Chong SY, Raja Ali RA, Amin Nordin S, Lee WS, Majid NA. Gut microbiota in early life and its influence on health and disease: A position paper by the Malaysian Working Group on Gastrointestinal Health. J Paediatr Child Health 2017; 53:1152-1158. [PMID: 29205651 DOI: 10.1111/jpc.13640] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/03/2017] [Accepted: 05/28/2017] [Indexed: 12/16/2022]
Abstract
The role of gut microbiota in early life and its impact on gut health and subsequent diseases remain unclear. There is a lack of research and awareness in this area, especially in the Asia-Pacific region, including Malaysia. This paper reports the position of a Malaysian Working Group on some key issues surrounding gut microbiota in early life and its role in gut health and diseases, as well as experts' stand on probiotics and prebiotics. The group reached a consensus that certain factors, including elective caesarean; premature deliveries; complementary feeding; use of antibiotics, prebiotics and/or probiotics; and exposure to the external environmental, have an impact on gut microbiota in early life. However, as evidence is lacking, especially from the Asia-Pacific region, further studies are needed to understand how gut microbiota in early life affects subsequent diseases, including allergy, inflammatory bowel disease, obesity and infantile colic. Lastly, although beneficial in acute diarrhoeal disease and probably allergic eczema, probiotics (and/or prebiotics) should be used cautiously in other gut dysbiotic conditions until more data are available.
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Affiliation(s)
- Yeong Yeh Lee
- School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Kelantan, Malaysia
| | - Siti Asma Hassan
- School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Kelantan, Malaysia
| | - Intan Hakimah Ismail
- Department of Paediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Sze Yee Chong
- Department of Paediatrics, Hospital Pulau Pinang, Georgetown, Pulau Pinang, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Syafinaz Amin Nordin
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Way Seah Lee
- Department of Paediatrics, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Noorizan Abdul Majid
- School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu, Kelantan, Malaysia
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119
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Knutie SA, Gabor CR, Kohl KD, Rohr JR. Do host-associated gut microbiota mediate the effect of an herbicide on disease risk in frogs? J Anim Ecol 2017; 87:489-499. [PMID: 29030867 DOI: 10.1111/1365-2656.12769] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 09/21/2017] [Indexed: 12/21/2022]
Abstract
Environmental stressors, such as pollutants, can increase disease risk in wildlife. For example, the herbicide atrazine affects host defences (e.g. resistance and tolerance) of the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), but the mechanisms for these associations are not entirely clear. Given that pollutants can alter the gut microbiota of hosts, which in turn can affect their health and immune systems, one potential mechanism by which pollutants could increase infection risk is by influencing host-associated microbiota. Here, we test whether early-life exposure to the estimated environmental concentration (EEC; 200 μg/L) of atrazine affects the gut bacterial composition of Cuban tree frog (Osteopilus septentrionalis) tadpoles and adults and whether any atrazine-induced change in community composition might affect host defences against Bd. We also determine whether early-life changes in the stress hormone corticosterone affect gut microbiota by experimentally inhibiting corticosterone synthesis with metyrapone. With the exception of changing the relative abundances of two bacterial genera in adulthood, atrazine did not affect gut bacterial diversity or community composition of tadpoles (in vivo or in vitro) or adults. Metyrapone did not significantly affect bacterial diversity of tadpoles, but significantly increased bacterial diversity of adults. Gut bacterial diversity during Bd exposure did not predict host tolerance or resistance to Bd intensity in tadpoles or adults. However, early-life bacterial diversity negatively predicted Bd intensity as adult frogs. Specifically, Bd intensity as adults was associated negatively with the relative abundance of phylum Fusobacteria in the guts of tadpoles. Our results suggest that the effect of atrazine on Bd infection risk is not mediated by host-associated microbiota because atrazine does not affect microbiota of tadpoles or adults. However, host-associated microbes seem important in host resistance to Bd because the early-life microbiota, during immune system development, predicted later-life infection risk with Bd. Overall, our study suggests that increasing gut bacterial diversity and relative abundances of Fusobacteria might have lasting positive effects on amphibian health.
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Affiliation(s)
- Sarah A Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Caitlin R Gabor
- Department of Biology, Texas State University, San Marcos, TX, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jason R Rohr
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
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120
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Functional Genomics of Host-Microbiome Interactions in Humans. Trends Genet 2017; 34:30-40. [PMID: 29107345 DOI: 10.1016/j.tig.2017.10.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 02/06/2023]
Abstract
The human microbiome has been linked to various host phenotypes and has been implicated in many complex human diseases. Recent genome-wide association studies (GWASs) have used microbiome variation as a complex trait and have uncovered human genetic variants that are associated with the microbiome. Here we summarize results from these studies and illustrate potential regulatory mechanisms by which host genetic variation can interact with microbiome composition. We argue that, similar to human GWASs, it is important to use functional genomics techniques to gain a mechanistic understanding of causal host-microbiome interactions and their role in human disease. We highlight experimental, functional, and computational genomics methodologies for the study of the genomic basis of host-microbiome interactions and describe how these approaches can be utilized to explain how human genetic variation can modulate the effects of the microbiome on the host.
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121
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Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life. PLoS One 2017; 12:e0185569. [PMID: 28968427 PMCID: PMC5624699 DOI: 10.1371/journal.pone.0185569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/14/2017] [Indexed: 12/13/2022] Open
Abstract
Few studies have analyzed the gut microbiota of child in unindustrialized countries, but none during the first month of life. Stool samples were collected from healthy newborns in hospitals of Gabon (n = 6) and Republic of the Congo (n = 9) at different time points during the first month of life: meconium, day 2 (D02), day 7 (D07) and day 28 (D28). In addition, one fecal sample was collected from each mother after delivery. Metagenomic sequencing was performed to determine the bacterial communities, and multiplex real-time PCR was used to detect the presence of seven enteric viruses (rotavirus a, adenovirus, norovirus I and II, sapovirus, astrovirus, enterovirus) in these samples. Bacterial diversity was high in the first days of life, and was dominated by the genus Prevotella. Then, it rapidly decreased and remained low up to D28 when the gut flora was composed almost exclusively of strictly anaerobic bacteria. Each infant’s fecal bacterial microbiota composition was significantly closer to that of their mother than to that of any other woman in the mothers’ group, suggesting an intrauterine, placental or amniotic fluid origin of such bacteria. Moreover, bacterial communities differed according to the delivery mode. Overall, the bacterial microbiota communities displayed a similar diversification and expansion in newborns within and between countries during the first four weeks of life. Moreover, six of the fifteen infants of this study harbored enteric viruses (rotavirus, enterovirus and adenovirus) in fecal samples, but never in the meconium. A maternal source for the viruses detected at D02 and D07 can be excluded because none of them was found also in the child’s mother. These findings improve our knowledge on the gut bacterial and viral communities of infants from two Sub-Saharan countries during their first month of life.
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122
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Chabé M, Lokmer A, Ségurel L. Gut Protozoa: Friends or Foes of the Human Gut Microbiota? Trends Parasitol 2017; 33:925-934. [PMID: 28870496 DOI: 10.1016/j.pt.2017.08.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/17/2017] [Accepted: 08/11/2017] [Indexed: 12/18/2022]
Abstract
The importance of the gut microbiota for human health has sparked a strong interest in the study of the factors that shape its composition and diversity. Despite the growing evidence suggesting that helminths and protozoa significantly interact with gut bacteria, gut microbiome studies remain mostly focused on prokaryotes and on populations living in industrialized countries that typically have a low parasite burden. We argue that protozoa, like helminths, represent an important factor to take into account when studying the gut microbiome, and that their presence - especially considering their long coevolutionary history with humans - may be beneficial. From this perspective, we examine the relationship between the protozoa and their hosts, as well as their relevance for public health.
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Affiliation(s)
- Magali Chabé
- University of Lille, CNRS, Inserm, CHU de Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Ana Lokmer
- UMR 7206 Eco-anthropologie et ethnobiologie, CNRS - MNHN - Paris Diderot University - Sorbonne Paris Cité, Paris, France
| | - Laure Ségurel
- UMR 7206 Eco-anthropologie et ethnobiologie, CNRS - MNHN - Paris Diderot University - Sorbonne Paris Cité, Paris, France.
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123
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Zhang M, Sun K, Wu Y, Yang Y, Tso P, Wu Z. Interactions between Intestinal Microbiota and Host Immune Response in Inflammatory Bowel Disease. Front Immunol 2017; 8:942. [PMID: 28855901 PMCID: PMC5558048 DOI: 10.3389/fimmu.2017.00942] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract. Although the etiology and pathogenesis of IBD remain unclear, both genetic susceptibility and environmental factors are implicated in the initiation and progression of IBD. Recent studies with experimental animal models and clinical patients indicated that the intestinal microbiota is one of the critical environmental factors that influence nutrient metabolism, immune responses, and the health of the host in various intestinal diseases, including ulcerative colitis and Crohn’s disease. The objective of this review is to highlight the crosstalk between gut microbiota and host immune response and the contribution of this interaction to the pathogenesis of IBD. In addition, potential therapeutic strategies targeting the intestinal micro-ecosystem in IBD are discussed.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China
| | - Kaiji Sun
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China
| | - Yujun Wu
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China
| | - Ying Yang
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China
| | - Patrick Tso
- Department of Pathology and Laboratory Medicine, Metabolic Diseases Institute, University of Cincinnati, Cincinnati, OH, United States
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China
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124
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Burgess SL, Gilchrist CA, Lynn TC, Petri WA. Parasitic Protozoa and Interactions with the Host Intestinal Microbiota. Infect Immun 2017; 85:e00101-17. [PMID: 28584161 PMCID: PMC5520446 DOI: 10.1128/iai.00101-17] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Parasitic protozoan infections represent a major health burden in the developing world and contribute significantly to morbidity and mortality. These infections are often associated with considerable variability in clinical presentation. An emerging body of work suggests that the intestinal microbiota may help to explain some of these differences in disease expression. The objective of this minireview is to synthesize recent progress in this rapidly advancing field. Studies of humans and animals and in vitro studies of the contribution of the intestinal microbiota to infectious disease are discussed. We hope to provide an understanding of the human-protozoal pathogen-microbiome interaction and to speculate on how that might be leveraged for treatment.
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Affiliation(s)
- Stacey L Burgess
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Carol A Gilchrist
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Tucker C Lynn
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
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125
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Gupta VK, Paul S, Dutta C. Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity. Front Microbiol 2017; 8:1162. [PMID: 28690602 PMCID: PMC5481955 DOI: 10.3389/fmicb.2017.01162] [Citation(s) in RCA: 573] [Impact Index Per Article: 81.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 06/07/2017] [Indexed: 12/14/2022] Open
Abstract
One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics or his environment. Some of the geographical/racial variations in microbiome structure have been attributed to differences in host genetics and innate/adaptive immunity, while in many other cases, cultural/behavioral features like diet, hygiene, parasitic load, environmental exposure etc. overshadow genetics. The ethnicity or population-specific variations in human microbiome composition, as reviewed in this report, question the universality of the microbiome-based therapeutic strategies and recommend for geographically tailored community-scale approaches to microbiome engineering.
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Affiliation(s)
- Vinod K Gupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical BiologyKolkata, India.,Academy of Scientific and Innovative ResearchKolkata, India
| | - Sandip Paul
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical BiologyKolkata, India
| | - Chitra Dutta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical BiologyKolkata, India.,Academy of Scientific and Innovative ResearchKolkata, India
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126
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Early exposure to agricultural soil accelerates the maturation of the early-life pig gut microbiota. Anaerobe 2017; 45:31-39. [DOI: 10.1016/j.anaerobe.2017.02.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 12/27/2022]
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127
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Moeller AH. The shrinking human gut microbiome. Curr Opin Microbiol 2017; 38:30-35. [PMID: 28458095 DOI: 10.1016/j.mib.2017.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 12/13/2022]
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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128
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Patterns in the skin microbiota differ in children and teenagers between rural and urban environments. Sci Rep 2017; 7:45651. [PMID: 28361981 PMCID: PMC5374497 DOI: 10.1038/srep45651] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/28/2017] [Indexed: 12/11/2022] Open
Abstract
The composition of human microbiota is affected by a multitude of factors. Understanding the dynamics of our microbial communities is important for promoting human health because microbiota has a crucial role in the development of inflammatory diseases, such as allergies. We have studied the skin microbiota of both arms in 275 Finnish children of few months old to teenagers living in contrasting environments. We show that while age is a major factor affecting skin microbial composition, the living environment also discriminates the skin microbiota of rural and urban children. The effect of environment is age-specific; it is most prominent in toddlers but weaker for newborns and non-existent for teenagers. Within-individual variation is also related to age and environment. Surprisingly, variation between arms is smaller in rural subjects in all age groups, except in teenagers. We also collected serum samples from children for characterization of allergic sensitization and found a weak, but significant association between allergic sensitization and microbial composition. We suggest that physiological and behavioral changes, related to age and the amount of contact with environmental microbiota, jointly influence the dynamics of the skin microbiota, and explain why the association between the living environment skin microbiota is lost in teenager.
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129
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Certad G, Viscogliosi E, Chabé M, Cacciò SM. Pathogenic Mechanisms of Cryptosporidium and Giardia. Trends Parasitol 2017; 33:561-576. [PMID: 28336217 DOI: 10.1016/j.pt.2017.02.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 02/07/2023]
Abstract
Intestinal protozoa are important etiological agents of diarrhea, particularly in children, yet the public health risk they pose is often neglected. Results from the Global Enteric Multicenter Study (GEMS) showed that Cryptosporidium is among the leading causes of moderate to severe diarrhea in children under 2 years. Likewise, Giardia infects approximately 200 million individuals worldwide, and causes acute diarrhea in children under 5 years. Despite this recognized role as pathogens, the question is why and how these parasites cause disease in some individuals but not in others. This review focuses on known pathogenic mechanisms of Cryptosporidium and Giardia, and infection progress towards disease.
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Affiliation(s)
- Gabriela Certad
- University of Lille, CNRS, Inserm, CHU Lille, Pasteur Institute of Lille, U1019-UMR 8204-CIIL, Center for Infection and Immunity of Lille, Lille, France; Medical Research Department, Hospital Group of the Catholic Institute of Lille, Faculty of Medicine and Maieutics, Catholic University of Lille, Lille, France.
| | - Eric Viscogliosi
- University of Lille, CNRS, Inserm, CHU Lille, Pasteur Institute of Lille, U1019-UMR 8204-CIIL, Center for Infection and Immunity of Lille, Lille, France
| | - Magali Chabé
- University of Lille, CNRS, Inserm, CHU Lille, Pasteur Institute of Lille, U1019-UMR 8204-CIIL, Center for Infection and Immunity of Lille, Lille, France
| | - Simone M Cacciò
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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130
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Crittenden AN, Schnorr SL. Current views on hunter‐gatherer nutrition and the evolution of the human diet. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162 Suppl 63:84-109. [DOI: 10.1002/ajpa.23148] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 11/03/2016] [Accepted: 11/15/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Alyssa N. Crittenden
- Laboratory of Metabolism, Anthropometry, and Nutrition, Department of AnthropologyUniversity of NevadaLas Vegas, Las Vegas Nevada
| | - Stephanie L. Schnorr
- Laboratories of Molecular Anthropology and Microbiome Research, Department of AnthropologyUniversity of OklahomaNorman Oklahoma
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131
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Abstract
The human gut microbial diversity has been reported to be lower in industrialized populations as compared to non-industrialized ones. Since it is also reduced in individuals with some metabolic and inflammatory diseases as compared to healthy ones, this "loss" of diversity in industrialized populations is currently considered to be a public health issue. However, little is known on the mechanisms that are causing this pattern. Is it due to differences in diet, sanitation, medication, host genetics, and/or other unidentified factors? In this review, we propose that part of this decrease in diversity is driven by latitude, as all studied industrialized countries are in higher latitudes than non-industrialized ones, and latitude is known to correlate with species diversity. Reanalyzing available data, we find that part of the gut microbial diversity is significantly correlated with latitude, which might therefore exacerbate the effect of lifestyle. Intriguingly, the observation of a higher diversity in industrialized countries has not been replicated in other human microbiomes.
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Affiliation(s)
- Emma Dikongué
- Eco-anthropologie et ethnobiologie, UMR 7206 CNRS - MNHN - Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et ethnobiologie, UMR 7206 CNRS - MNHN - Univ Paris Diderot, Sorbonne Paris Cité, Paris, France
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132
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Microbiome and chronic inflammatory bowel diseases. J Mol Med (Berl) 2016; 95:21-28. [PMID: 27988792 DOI: 10.1007/s00109-016-1495-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/15/2016] [Accepted: 11/25/2016] [Indexed: 01/12/2023]
Abstract
It is nowadays generally accepted that the microbiome is a central driver of chronic inflammatory bowel diseases based on observations from human patients as well as inflammatory rodent models. Many studies focussed on different aspects of microbiota and some scientists believe that a primary dis-balance results in a direct microbial induced inflammatory situation. It is also clear that the microbiome is influenced by environmental and genetic factors and is also tightly regulated by host defense molecules such as antimicrobial peptides (defensins et al.). Different lines of investigations showed different complex antimicrobial barrier defects in inflammatory bowel diseases which also influence the composition of the microbiome and generally impact on the microbial-mucosal interface. In this review, we aim to discuss the bigger picture of these different aspects and current views and conclude about therapeutic consequences for future concepts beyond anti-inflammatory treatment.
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133
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Bhattacharjee S, Kalbfuss N, Prazeres da Costa C. Parasites, microbiota and metabolic disease. Parasite Immunol 2016; 39. [DOI: 10.1111/pim.12390] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/03/2016] [Indexed: 12/28/2022]
Affiliation(s)
- S. Bhattacharjee
- Institute for Medical Microbiology, Immunology and Hygiene; Technische Universität München (TUM); München Germany
| | - N. Kalbfuss
- Institute for Medical Microbiology, Immunology and Hygiene; Technische Universität München (TUM); München Germany
| | - C. Prazeres da Costa
- Institute for Medical Microbiology, Immunology and Hygiene; Technische Universität München (TUM); München Germany
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134
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Beltrame MH, Rubel MA, Tishkoff SA. Inferences of African evolutionary history from genomic data. Curr Opin Genet Dev 2016; 41:159-166. [PMID: 27810637 PMCID: PMC5161638 DOI: 10.1016/j.gde.2016.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/29/2016] [Accepted: 10/07/2016] [Indexed: 01/22/2023]
Abstract
Africa is the origin of anatomically modern humans and a continent of linguistic, cultural, environmental, phenotypic, and genetic diversity. However, African populations remain underrepresented in genetic studies, which have largely focused on individuals with European and Asian ancestry. The expansion of high-throughput 'omic' technologies to interrogate multiple tissue types across many biomolecules-DNA, proteins, epigenetic modifications, metabolites, and others-has heralded a new era of investigation into African history. In this review, we summarize how some of these recent advances have been applied to contemporary sub-Saharan African populations to inform studies on human origins and adaptation.
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Affiliation(s)
- Marcia Holsbach Beltrame
- Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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135
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Vilajeliu-Pons A, Bañeras L, Puig S, Molognoni D, Vilà-Rovira A, Hernández-del Amo E, Balaguer MD, Colprim J. External Resistances Applied to MFC Affect Core Microbiome and Swine Manure Treatment Efficiencies. PLoS One 2016; 11:e0164044. [PMID: 27701451 PMCID: PMC5049776 DOI: 10.1371/journal.pone.0164044] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022] Open
Abstract
Microbial fuel cells (MFCs) can be designed to combine water treatment with concomitant electricity production. Animal manure treatment has been poorly explored using MFCs, and its implementation at full-scale primarily relies on the bacterial distribution and activity within the treatment cell. This study reports the bacterial community changes at four positions within the anode of two almost identically operated MFCs fed swine manure. Changes in the microbiome structure are described according to the MFC fluid dynamics and the application of a maximum power point tracking system (MPPT) compared to a fixed resistance system (Ref-MFC). Both external resistance and cell hydrodynamics are thought to heavily influence MFC performance. The microbiome was characterised both quantitatively (qPCR) and qualitatively (454-pyrosequencing) by targeting bacterial 16S rRNA genes. The diversity of the microbial community in the MFC biofilm was reduced and differed from the influent swine manure. The adopted electric condition (MPPT vs fixed resistance) was more relevant than the fluid dynamics in shaping the MFC microbiome. MPPT control positively affected bacterial abundance and promoted the selection of putatively exoelectrogenic bacteria in the MFC core microbiome (Sedimentibacter sp. and gammaproteobacteria). These differences in the microbiome may be responsible for the two-fold increase in power production achieved by the MPPT-MFC compared to the Ref-MFC.
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Affiliation(s)
| | - Lluis Bañeras
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, Girona, Spain
- * E-mail:
| | - Sebastià Puig
- LEQUiA, Institute of the Environment, University of Girona, Girona, Spain
| | - Daniele Molognoni
- Department of Civil Engineering and Architecture (D.I.C.Ar.), University of Pavia, Pavia, Italy
| | - Albert Vilà-Rovira
- LEQUiA, Institute of the Environment, University of Girona, Girona, Spain
| | - Elena Hernández-del Amo
- Molecular Microbial Ecology Group, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Maria D. Balaguer
- LEQUiA, Institute of the Environment, University of Girona, Girona, Spain
| | - Jesús Colprim
- LEQUiA, Institute of the Environment, University of Girona, Girona, Spain
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136
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Schnorr SL, Sankaranarayanan K, Lewis CM, Warinner C. Insights into human evolution from ancient and contemporary microbiome studies. Curr Opin Genet Dev 2016; 41:14-26. [PMID: 27507098 DOI: 10.1016/j.gde.2016.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA.
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137
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Abstract
Entamoeba histolytica, the etiological agent of amebiasis, is a significant cause of pediatric diarrhea in South Asia and sub-Saharan Africa. The clinical outcome of an E. histolytica exposure varies enormously and can present as diarrhea, dysentery, or amebic liver abscess. Host and parasite factors likely contribute to the outcome of infection with the parasite, but do not explain the wide variation in presentation of disease. This suggests that other environmental factors affect disease. An emerging body of work suggests that the host intestinal bacterial microbiome may have a significant influence on the development and outcome of amebiasis.
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Affiliation(s)
- Stacey L. Burgess
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA USA
| | - William A. Petri
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA USA
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138
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Mosca A, Leclerc M, Hugot JP. Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem? Front Microbiol 2016; 7:455. [PMID: 27065999 PMCID: PMC4815357 DOI: 10.3389/fmicb.2016.00455] [Citation(s) in RCA: 346] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/21/2016] [Indexed: 12/12/2022] Open
Abstract
Most of the Human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota. The Western way of life, with a wide use of antibiotics and other environmental triggers, may reduce the number of bacterial predators leading to a decrease in microbial diversity of the Human gut. We argue that this phenomenon is similar to the process of ecosystem impoverishment in macro ecology where human activity decreases ecological niches, the size of predator populations, and finally the biodiversity. Such pauperization is fundamental since it reverses the evolution processes, drives life backward into diminished complexity, stability, and adaptability. A simple therapeutic approach could thus be to reintroduce bacterial predators and restore a bacterial diversity of the host microbiota.
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Affiliation(s)
- Alexis Mosca
- Hôpital Robert Debré, Assistance Publique-Hopitaux de ParisParis, France; Institut National de la Santé et de la Recherche Médicale et Université Paris Diderot, Sorbonne Paris-Cité, United Medical Resources 1149 Labex InflamexParis, France
| | - Marion Leclerc
- INRA, AgroParisTech, United Medical Resources 1319 MICALIS Paris, France
| | - Jean P Hugot
- Hôpital Robert Debré, Assistance Publique-Hopitaux de ParisParis, France; Institut National de la Santé et de la Recherche Médicale et Université Paris Diderot, Sorbonne Paris-Cité, United Medical Resources 1149 Labex InflamexParis, France
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139
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Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Rep 2016; 14:2142-2153. [PMID: 26923597 DOI: 10.1016/j.celrep.2016.02.013] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 12/07/2015] [Accepted: 01/28/2016] [Indexed: 12/20/2022] Open
Abstract
To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.
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Affiliation(s)
- Andres Gomez
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno 603 65, Czech Republic; Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Liberec Zoo, Liberec 460 01, Czech Republic
| | - Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Klara Vlckova
- Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - David Modry
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic; CEITEC, Central European Institute for Technology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - Angelique Todd
- Dzanga-Sangha Protected Areas, World Wildlife Fund, Bayanga, Central African Republic
| | | | - Melissa J Remis
- Department of Anthropology, Purdue University, West Lafayette, IN 47907, USA
| | | | - Elise Morton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Juan D Umaña
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AK 72704, USA
| | - H Rex Gaskins
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Brenda A Wilson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rebecca M Stumpf
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bryan A White
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steven R Leigh
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Colorado, Boulder, CO 80309, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
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