151
|
The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche. ISME JOURNAL 2018; 12:728-741. [PMID: 29374268 DOI: 10.1038/s41396-017-0003-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/20/2017] [Accepted: 10/09/2017] [Indexed: 01/13/2023]
Abstract
Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypothesized that unsuccessful invasions can cause impacts to soil functioning by decreasing the diversity and niche breadth of resident bacterial communities, which could cause shifts to community composition and niche structure-an effect that is likely exacerbated when diversity is compromised. To examine this question, diversity gradients of soil microbial communities were subjected to invasion by the frequent, yet oft-unsuccessful soil invader, Escherichia coli, and evaluated for changes to diversity, bacterial community composition, niche breadth, and niche structure. Contrary to expectations, diversity and niche breadth increased across treatments upon invasion. Community composition and niche structure were also altered, with shifts of niche structure revealing an escape by the resident community away from the invader's resources. Importantly, the extent of the escape varied in response to the community's diversity, where less diverse communities experienced larger shifts. Thus, although transient and unsuccessful, the invader competed for resources with resident species and caused tangible impacts that modified both the diversity and functioning of resident communities, which can likely generate a legacy effect that influences future invasion attempts.
Collapse
|
152
|
Microbial treatment in chronic constipation. SCIENCE CHINA-LIFE SCIENCES 2018; 61:744-752. [PMID: 29388040 DOI: 10.1007/s11427-017-9220-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022]
Abstract
Chronic functional constipation is a kind of common intestinal disease that occurs in children, adults and elderly people. This disease not only causes great influence to physiological function, but also results in varying degrees of psychological barriers. At present, constipation treatments continue to rely on traditional methods such as purgative therapy and surgery. However, these approaches can disrupt intestinal function. Recent research between intestinal diseases and gut microbiota has gradually revealed a connection between constipation and intestinal flora disturbance, providing a theoretical basis for microbial treatment in chronic constipation. Microbial treatment mainly includes probiotic preparations such as probiotics, prebiotics, synbiotics and fecal microbiota transplantation (FMT). Due to its safety, convenience and curative effect, probiotic preparations have been widely accepted, especially gradually developed FMT with higher curative effects. Microbial treatment improves clinical symptoms, promotes the recovery of intestinal flora, and has no complications during the treatment process. Compared with traditional treatments, microbial treatment in chronic constipation has advantages, and is worthy of further promotion from clinical research to clinical application.
Collapse
|
153
|
Abstract
PURPOSE OF REVIEW An imbalance between pathogenic and protective microbiota characterizes dysbiosis. Presence of dysbiosis may affect immunity, tolerance, or disease depending on a variety of conditions. In the transplant patient population, the need for immunosuppression and widespread use of prophylactic and therapeutic antimicrobial agents create new posttransplant microbiota communities that remain to be fully defined. RECENT FINDINGS Studies in mice have demonstrated significant bidirectional interactions between microbiota-derived products and host immune cells. The stimulation of regulatory T cell and T helper cell type 17 cells by specific products leads to maintenance of immune homeostasis versus activation of inflammation, respectively. Dysbiosis may lead to development of antigen cross-reactivity, which may affect alloreactivity. Certain immunologic sequelae of microbiota are pronounced in chronic kidney disease, because of uremia and renal metabolism of microbiota metabolites. Dietary modifications, probiotics, and fecal microbiota transplant have been investigated for alteration of microbiota in humans. SUMMARY Researchers have begun to identify dysbioses associated with clinical conditions, including chronic kidney disease, posttransplant infection, and rejection. This information will allow clinicians not only to select at-risk patients for early intervention, but also to develop therapies that restore the microbiota to a state of homeostasis or tolerance.
Collapse
|
154
|
Paganini D, Zimmermann MB. The effects of iron fortification and supplementation on the gut microbiome and diarrhea in infants and children: a review. Am J Clin Nutr 2017; 106:1688S-1693S. [PMID: 29070552 PMCID: PMC5701709 DOI: 10.3945/ajcn.117.156067] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In infants and young children in Sub-Saharan Africa, iron-deficiency anemia (IDA) is common, and many complementary foods are low in bioavailable iron. In-home fortification of complementary foods using iron-containing micronutrient powders (MNPs) and oral iron supplementation are both effective strategies to increase iron intakes and reduce IDA at this age. However, these interventions produce large increases in colonic iron because the absorption of their high iron dose (≥12.5 mg) is typically <20%. We reviewed studies in infants and young children on the effects of iron supplements and iron fortification with MNPs on the gut microbiome and diarrhea. Iron-containing MNPs and iron supplements can modestly increase diarrhea risk, and in vitro and in vivo studies have suggested that this occurs because increases in colonic iron adversely affect the gut microbiome in that they decrease abundances of beneficial barrier commensal gut bacteria (e.g., bifidobacteria and lactobacilli) and increase the abundance of enterobacteria including entropathogenic Escherichia coli These changes are associated with increased gut inflammation. Therefore, safer formulations of iron-containing supplements and MNPs are needed. To improve MNP safety, the iron dose of these formulations should be reduced while maximizing absorption to retain efficacy. Also, the addition of prebiotics to MNPs is a promising approach to mitigate the adverse effects of iron on the infant gut.
Collapse
Affiliation(s)
- Daniela Paganini
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Michael B Zimmermann
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
155
|
Anderson CJ, Kendall MM. Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation. Front Microbiol 2017; 8:1983. [PMID: 29075247 PMCID: PMC5643478 DOI: 10.3389/fmicb.2017.01983] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial pathogens must sense and respond to newly encountered host environments to regulate the expression of critical virulence factors that allow for niche adaptation and successful colonization. Among bacterial pathogens, non-typhoidal serovars of Salmonella enterica, such as serovar Typhimurium (S. Tm), are a primary cause of foodborne illnesses that lead to hospitalizations and deaths worldwide. S. Tm causes acute inflammatory diarrhea that can progress to invasive systemic disease in susceptible patients. The gastrointestinal tract and intramacrophage environments are two critically important niches during S. Tm infection, and each presents unique challenges to limit S. Tm growth. The intestinal tract is home to billions of commensal microbes, termed the microbiota, which limits the amount of available nutrients for invading pathogens such as S. Tm. Therefore, S. Tm encodes strategies to manipulate the commensal population and side-step this nutritional competition. During subsequent stages of disease, S. Tm resists host immune cell mechanisms of killing. Host cells use antimicrobial peptides, acidification of vacuoles, and nutrient limitation to kill phagocytosed microbes, and yet S. Tm is able to subvert these defense systems. In this review, we discuss recently described molecular mechanisms that S. Tm uses to outcompete the resident microbiota within the gastrointestinal tract. S. Tm directly eliminates close competitors via bacterial cell-to-cell contact as well as by stimulating a host immune response to eliminate specific members of the microbiota. Additionally, S. Tm tightly regulates the expression of key virulence factors that enable S. Tm to withstand host immune defenses within macrophages. Additionally, we highlight the chemical and physical signals that S. Tm senses as cues to adapt to each of these environments. These strategies ultimately allow S. Tm to successfully adapt to these two disparate host environments. It is critical to better understand bacterial adaptation strategies because disruption of these pathways and mechanisms, especially those shared by multiple pathogens, may provide novel therapeutic intervention strategies.
Collapse
Affiliation(s)
- Christopher J Anderson
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
| | - Melissa M Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine,, Charlottesville, VA, United States
| |
Collapse
|
156
|
Zhang K, Griffiths G, Repnik U, Hornef M. Seeing is understanding: Salmonella's way to penetrate the intestinal epithelium. Int J Med Microbiol 2017; 308:97-106. [PMID: 28939439 DOI: 10.1016/j.ijmm.2017.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
The molecular processes that govern host-microbial interaction illustrate not only the sophisticated and multifaceted mechanisms that protect the host from infection, but also the elaborated features of microbial pathogens that have evolved to overcome or evade the host's immune system. Here we focus on Salmonella that like other enteric pathogens must overcome the intestinal mucosal immune system, a surface constantly on alert and evolved to restrict the enteric microbiota. We discuss the initial step of Salmonella infection, the penetration of the intestinal epithelial barrier and the models used to study this fascinating aspect of microbial pathogenesis.
Collapse
Affiliation(s)
- Kaiyi Zhang
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany
| | | | - Urska Repnik
- Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Mathias Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany.
| |
Collapse
|
157
|
Walter J, Maldonado-Gómez MX, Martínez I. To engraft or not to engraft: an ecological framework for gut microbiome modulation with live microbes. Curr Opin Biotechnol 2017; 49:129-139. [PMID: 28866242 DOI: 10.1016/j.copbio.2017.08.008] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 02/08/2023]
Abstract
Strategies aimed at modulating the gut microbiota by using live microbes range from single strains (probiotics or live biotherapeutics) to whole non-defined fecal transplants. Although often clinically efficacious, our understanding on how microbial-based strategies modulate gut microbiome composition and function is vastly incomplete. In this review, we present a framework based on ecological theory that provides mechanistic explanations for the findings obtained in studies that attempted to modulate the gut microbiota of humans and animals using live microbes. We argue that an ecological perspective grounded in theory is necessary to interpret and predict the impact of microbiome-modulating strategies and thus advance our ability to develop improved and targeted approaches with enhanced therapeutic efficiency.
Collapse
Affiliation(s)
- Jens Walter
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, AB, Canada; Department of Biological Sciences, University of Alberta, AB, Canada.
| | - María X Maldonado-Gómez
- Department of Food Science and Technology, University of California, Davis 95616, United States
| | - Inés Martínez
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, AB, Canada; Sacco System, Cadorago 22071, Italy
| |
Collapse
|
158
|
Nie L, Zhou QJ, Qiao Y, Chen J. Interplay between the gut microbiota and immune responses of ayu (Plecoglossus altivelis) during Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2017; 68:479-487. [PMID: 28756287 DOI: 10.1016/j.fsi.2017.07.054] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
Gut microbiota plays fundamental roles in protection against pathogen invasion. However, the mechanism and extent of responses of gut microbiota to pathogenic infection are poorly understood. This study investigated the gut bacterial communities and immune responses of ayu (Plecoglossus altivelis) upon exposure to Vibrio anguillarum. The succession of V. anguillarum infection was evidenced by increased expression of immune genes and bacterial loads in ayu tissues, which in turn altered the composition and predicted functions of gut bacterial community. The dynamics of gut bacterial diversity and evenness were temporally stable in control ayu but were reduced in infected subjects, particularly at the late stages of infection. Variations in the gut microbiota were significantly associated with the expression levels of TNF-α (P = 0.019) and IL-1 β (P = 0.013). The profiles of certain gut bacterial taxa were indicative of V. anguillarum infection. Compared with healthy controls, the ayu infected with V. anguillarum possessed less complex, fewer connected, and lower cooperative gut bacterial interspecies interaction, coinciding with significant shifts in keystone species. These findings imply that V. anguillarum infection substantially disrupted the compositions and interspecies interaction of ayu gut bacterial community, thereby altering gut microbial-mediated functions and inducing host immune responses. This study provides an integrated overview on the interaction between the gut microbiota and host immune responses to pathogen infection from an ecological perspective.
Collapse
Affiliation(s)
- Li Nie
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Qian-Jin Zhou
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Yan Qiao
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Jiong Chen
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
159
|
Diard M, Hardt WD. Basic Processes in Salmonella-Host Interactions: Within-Host Evolution and the Transmission of the Virulent Genotype. Microbiol Spectr 2017; 5:10.1128/microbiolspec.mtbp-0012-2016. [PMID: 28884670 PMCID: PMC11687551 DOI: 10.1128/microbiolspec.mtbp-0012-2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Indexed: 01/08/2023] Open
Abstract
Transmission and virulence are central aspects of pathogen evolution. However, in many cases their interconnection has proven difficult to assess by experimentation. Here we discuss recent advances from a mouse model for Salmonella diarrhea. Mouse models mimic the enhanced susceptibility of antibiotic-treated individuals to nontyphoidal salmonellosis. In streptomycin-pretreated mice, Salmonella enterica subspecies 1 serovar Typhimurium efficiently colonizes the gut lumen and elicits pronounced enteropathy. In the host's gut, S. Typhimurium forms two subpopulations that cooperate to elicit disease and optimize transmission. The disease-causing subpopulation expresses a set of dedicated virulence factors (the type 3 secretion system 1 [TTSS-1]) that drive gut tissue invasion. The virulence factor expression is "costly" by retarding the growth rate and exposing the pathogen to innate immune defenses within the gut tissue. These costs are compensated by the gut inflammation (a "public good") that is induced by the invading subpopulation. The inflamed gut lumen fuels S. Typhimurium growth, in particular that of the TTSS-1 "off" subpopulation. The latter grows up to very high densities and promotes transmission. Thus, both phenotypes cooperate to elicit disease and ensure transmission. This system has provided an experimental framework for studying within-host evolution of pathogen virulence, how cooperative virulence is stabilized, and how environmental changes (e.g., antibiotic therapy) affect the transmission of the virulent genotype.
Collapse
Affiliation(s)
- Médéric Diard
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
160
|
Palmer AD, Slauch JM. Mechanisms of Salmonella pathogenesis in animal models. HUMAN AND ECOLOGICAL RISK ASSESSMENT : HERA 2017; 23:1877-1892. [PMID: 31031557 PMCID: PMC6484827 DOI: 10.1080/10807039.2017.1353903] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Animal models play an important role in understanding the mechanisms of bacterial pathogenesis. Here we review recent studies of Salmonella infection in various animal models. Although mice are a classic animal model for Salmonella, mice do not normally get diarrhea, raising the question of how well the model represents normal human infection. However, pretreatment of mice with oral streptomycin, which apparently reduces the normal microbiota, leads to an inflammatory diarrheal response upon oral infection with Salmonella. This has led to a re-evaluation of the role of various Salmonella virulence factors in colonization of the intestine and induction of diarrhea. Indeed, it is now clear that Salmonella purposefully induces inflammation, which leads to the production of both carbon sources and terminal electron acceptors by the host that allow Salmonella to outgrow the normal intestinal microbiota. Overall use of this modified mouse model provides a more nuanced understanding of Salmonella intestinal infection in the context of the microbiota with implications for the ability to predict human risk.
Collapse
Affiliation(s)
- Alexander D Palmer
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - James M Slauch
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| |
Collapse
|
161
|
Yin X, Lee B, Zaragoza J, Marco ML. Dietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract. Sci Rep 2017; 7:7267. [PMID: 28779118 PMCID: PMC5544775 DOI: 10.1038/s41598-017-07428-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/23/2017] [Indexed: 12/18/2022] Open
Abstract
Host diet is a major determinant of the composition and function of the intestinal microbiome. Less understood is the importance of diet on ingested strains with probiotic significance. We investigated the population dynamics of exogenous Lactobacillus plantarum and its interactions with intestinal bacteria in mice undergoing switches between high-fat, high-sugar (HFHSD) and low-fat, plant-polysaccharide rich (LFPPD) diets. The survival and persistence of ingested L. plantarum WCFS1 was significantly improved during mouse consumption of HFHSD and was negatively associated with the numbers of indigenous Lactobacillus species. Diet also rapidly changed the composition of the indigenous microbiota, but with some taxa differentially affected between HFHSD periods. L. plantarum was not integrated into indigenous bacterial community networks according to co-occurrence patterns but still conferred distinct effects on bacterial species diversity and microbiota stability largely in a diet-dependent manner. Metagenome predictions supported the premise that L. plantarum dampens the effects of diet on the microbiome. This strain also consistently altered the predicted genetic content in the distal gut by enriching for genes encoding glyosyltransferases and bile salt hydrolases. Our findings demonstrate the interactions between ingested, transient probiotic bacteria and intestinal bacterial communities and how they can differ depending on host diet.
Collapse
Affiliation(s)
- Xiaochen Yin
- Department of Food Science and Technology, University of California, Davis, USA.,Department of Plant Pathology, Univeristy of California, Davis, CA, USA
| | - Bokyung Lee
- Department of Food Science and Technology, University of California, Davis, USA.,Center for Comparative Medicine, Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jose Zaragoza
- Department of Food Science and Technology, University of California, Davis, USA.,Bayer Crop Science, West Sacramento, CA, USA
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, USA.
| |
Collapse
|
162
|
Guo Y, Xun Z, Coffman SR, Chen F. The Shift of the Intestinal Microbiome in the Innate Immunity-Deficient Mutant rde-1 Strain of C. elegans upon Orsay Virus Infection. Front Microbiol 2017; 8:933. [PMID: 28611740 PMCID: PMC5446984 DOI: 10.3389/fmicb.2017.00933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/08/2017] [Indexed: 01/19/2023] Open
Abstract
The status of intestinal microbiota is a determinant of host health. However, the alteration of the gut microbiota caused by the innate immune response to virus infection is unclear. Caenorhabditis elegans and its natural virus Orsay provide an excellent model of host–virus interactions. We evaluated the intestinal microbial community complexity of the wild-type N2 and the innate immunity-deficient mutant rde-1 (ne219) strains of C. elegans upon Orsay virus infection. The gut microbiota diversity was decreased in rde-1 (ne219) mutant animals, and a large number of genes were associated with the difference between infected and uninfected rde-1 (ne219) mutant animals. Therefore, this study provides the first evaluation of the alterations caused by Orsay virus on intestinal microbiota in wildtype and innate immunity-deficient animals using C. elegans as the model species. Our findings indicate that virus infection may alters the microbiome in animals with defective immune response.
Collapse
Affiliation(s)
- Yuanyuan Guo
- School of Life Science, Peking UniversityBeijing, China
| | - Zhe Xun
- Central Laboratory, Peking University School of StomatologyBeijing, China
| | | | - Feng Chen
- Central Laboratory, Peking University School of StomatologyBeijing, China
| |
Collapse
|
163
|
Almonacid DE, Kraal L, Ossandon FJ, Budovskaya YV, Cardenas JP, Bik EM, Goddard AD, Richman J, Apte ZS. 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. PLoS One 2017; 12:e0176555. [PMID: 28467461 PMCID: PMC5414997 DOI: 10.1371/journal.pone.0176555] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/12/2017] [Indexed: 12/12/2022] Open
Abstract
Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions. We evaluated the possibility of detecting 46 clinical prokaryotic targets in the human gut, 28 of which could be identified with high precision and sensitivity by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. These targets included 20 commensal, 3 beneficial (probiotic), and 5 pathogenic intestinal microbial taxa. Using stool microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay quantifies 28 targets in the context of a healthy reference range and correctly reflected 38/38 verification samples of real and synthetic stool material containing known gut pathogens. Thus, we have established a method to determine microbiome composition with a focus on clinically relevant taxa, which has the potential to contribute to patient diagnosis, treatment, and monitoring. More broadly, our method can facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.
Collapse
Affiliation(s)
| | - Laurens Kraal
- uBiome, Inc., San Francisco, California, United States of America
| | | | | | | | - Elisabeth M Bik
- uBiome, Inc., San Francisco, California, United States of America
| | - Audrey D Goddard
- uBiome, Inc., San Francisco, California, United States of America
| | - Jessica Richman
- uBiome, Inc., San Francisco, California, United States of America
| | - Zachary S Apte
- uBiome, Inc., San Francisco, California, United States of America.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| |
Collapse
|
164
|
Xiong J, Dai W, Zhu J, Liu K, Dong C, Qiu Q. The Underlying Ecological Processes of Gut Microbiota Among Cohabitating Retarded, Overgrown and Normal Shrimp. MICROBIAL ECOLOGY 2017; 73:988-999. [PMID: 27966036 DOI: 10.1007/s00248-016-0910-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Increasing evidence of tight links among the gut microbiota, obesity, and host health has emerged, but knowledge of the ecological processes that shape the variation in microbial assemblages across growth rates remains elusive. Moreover, inadequately control for differences in factors that profoundly affect the gut microbial community, hampers evaluation of the gut microbiota roles in regulating growth rates. To address this gap, we evaluated the composition and ecological processes of the gut bacterial community in cohabitating retarded, overgrown, and normal shrimps from identically managed ponds. Gut bacterial community structures were distinct (P = 0.0006) among the shrimp categories. Using a structural equation modeling (SEM), we found that changes in the gut bacterial community were positively related to digestive activities, which subsequently affected shrimp growth rate. This association was further supported by intensified interspecies interaction and enriched lineages with high nutrient intake efficiencies in overgrown shrimps. However, the less phylogenetic clustering of gut microbiota in overgrown and retarded subjects may offer empty niches for pathogens invasion, as evidenced by higher abundances of predicted functional pathways involved in disease infection. Given no differences in biotic and abiotic factors among the cohabitating shrimps, we speculated that the distinct gut community assembly could be attributed to random colonization in larval shrimp (e.g., priority effects) and that an altered microbiota could be a causative factor in overgrowth or retardation in shrimp. To our knowledge, this is the first study to provide an integrated overview of the direct roles of gut microbiota in shaping shrimp growth rate and the underlying ecological mechanisms.
Collapse
Affiliation(s)
- Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
| | - Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Jinyong Zhu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Keshao Liu
- Key Laboratory of Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen, 361006, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| |
Collapse
|
165
|
Wotzka SY, Nguyen BD, Hardt WD. Salmonella Typhimurium Diarrhea Reveals Basic Principles of Enteropathogen Infection and Disease-Promoted DNA Exchange. Cell Host Microbe 2017; 21:443-454. [PMID: 28407482 DOI: 10.1016/j.chom.2017.03.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/17/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022]
Abstract
Despite decades of research, efficient therapies for most enteropathogenic bacteria are still lacking. In this review, we focus on Salmonella enterica Typhimurium (S. Typhimurium), a frequent cause of acute, self-limiting food-borne diarrhea and a model that has revealed key principles of enteropathogen infection. We review the steps of gut infection and the mucosal innate-immune defenses limiting pathogen burdens, and we discuss how inflammation boosts gut luminal S. Typhimurium growth. We also discuss how S. Typhimurium-induced inflammation accelerates the transfer of plasmids and phages, which may promote the transmission of antibiotic resistance and facilitate emergence of pathobionts and pathogens with enhanced virulence. The targeted manipulation of the microbiota and vaccination might offer strategies to prevent this evolution. As gut luminal microbes impact various aspects of the host's physiology, improved strategies for preventing enteropathogen infection and disease-inflicted DNA exchange may be of broad interest well beyond the acute infection.
Collapse
Affiliation(s)
- Sandra Y Wotzka
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bidong D Nguyen
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | | |
Collapse
|
166
|
Borton MA, Sabag-Daigle A, Wu J, Solden LM, O’Banion BS, Daly RA, Wolfe RA, Gonzalez JF, Wysocki VH, Ahmer BMM, Wrighton KC. Chemical and pathogen-induced inflammation disrupt the murine intestinal microbiome. MICROBIOME 2017; 5:47. [PMID: 28449706 PMCID: PMC5408407 DOI: 10.1186/s40168-017-0264-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/11/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Salmonella is one of the most significant food-borne pathogens to affect humans and agriculture. While it is well documented that Salmonella infection triggers host inflammation, the impacts on the gut environment are largely unknown. A CBA/J mouse model was used to evaluate intestinal responses to Salmonella-induced inflammation. In parallel, we evaluated chemically induced inflammation by dextran sodium sulfate (DSS) and a non-inflammation control. We profiled gut microbial diversity by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from fecal and cecal samples. These data were correlated to the inflammation marker lipocalin-2 and short-chain fatty acid concentrations. RESULTS We demonstrated that inflammation, chemically or biologically induced, restructures the chemical and microbial environment of the gut over a 16-day period. We observed that the ten mice within the Salmonella treatment group had a variable Salmonella relative abundance, with three high responding mice dominated by >46% Salmonella at later time points and the remaining seven mice denoted as low responders. These low- and high-responding Salmonella groups, along with the chemical DSS treatment, established an inflammation gradient with chemical and low levels of Salmonella having at least 3 log-fold lower lipocalin-2 concentration than the high-responding Salmonella mice. Total short-chain fatty acid and individual butyrate concentrations each negatively correlated with inflammation levels. Microbial communities were also structured along this inflammation gradient. Low levels of inflammation, regardless of chemical or biological induction, enriched for Akkermansia spp. in the Verrucomicrobiaceae and members of the Bacteroidetes family S24-7. Relative to the control or low inflammation groups, high levels of Salmonella drastically decreased the overall microbial diversity, specifically driven by the reduction of Alistipes and Lachnospiraceae in the Bacteroidetes and Firmicutes phyla, respectively. Conversely, members of the Enterobacteriaceae and Lactobacillus were positively correlated to high levels of Salmonella-induced inflammation. CONCLUSIONS Our results show that enteropathogenic infection and intestinal inflammation are interrelated factors modulating gut homeostasis. These findings may prove informative with regard to prophylactic or therapeutic strategies to prevent disruption of microbial communities, or promote their restoration.
Collapse
Affiliation(s)
- Mikayla A. Borton
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Jikang Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 USA
| | - Lindsey M. Solden
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Bridget S. O’Banion
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Rebecca A. Daly
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Richard A. Wolfe
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| | - Juan F. Gonzalez
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 USA
| | - Brian M. M. Ahmer
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210 USA
- Center for Microbial Interface Biology, The Ohio State University, Columbus, OH 43210 USA
| | - Kelly C. Wrighton
- Department of Microbiology, The Ohio State University, 484 W. 12th Avenue, 440 Biological Sciences Building, Columbus, OH 43210 USA
| |
Collapse
|
167
|
Galvão M, Bastos R, Acurcio L, Nascimento B, Sandes S, Arantes R, Souza M, Martins F, Vieira L, Nicoli J. Evaluation of colonisation resistance in stool of human donors using ex vivo, in vitro and in vivo assays. Benef Microbes 2017; 8:217-230. [DOI: 10.3920/bm2016.0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The indigenous microbiota is the population of microorganisms normally present on the surface and mucosa of an individual, where it performs essential health functions, including the colonisation resistance (CR) against pathogens. To identify the bacteria responsible and the mechanisms involved in the CR, the germ-free (GF) animal model has been used, because in vitro studies cannot always be extrapolated to what occurs in vivo. In this study, ex vivo antagonism assays against seven enteropathogenic bacteria using stools from 15 healthy human donors confirmed that the CR showed individual variation. Using in vitro antagonism assays, 14 strains isolated from dominant faecal microbiota of donors with elevated CR were selected for mono-association in GF mice to test the in vivo antagonism against Salmonella enterica ser. Typhimurium. Mice mono-associated with Enterococcus hirae strain 8.2, Bacteroides thetaiotaomicron strain 16.2 and Lactobacillus ruminis strain 18.1 had significant reductions in faecal counts of the pathogen during the challenge. After five days of infection, the group associated with E. hirae 8.2 showed a reduction in the translocation of S. Typhimurium to the spleen, while the group associated with L. ruminis 18.1 presented an increased translocation to the liver. The histological data confirmed these results and revealed that the mice associated with E. hirae 8.2 showed fewer lesions on ileum and liver, compared to the damage caused by S. Typhimurium alone, while in mice associated with L. ruminis 18.1 there was significantly worse lesions. Concluding, from the dominant faecal microbiota from healthy human with high CR, through ex vivo, in vitro and in vivo assays, a bacterium was characterised for its high CR potential, being a candidate for probiotic use.
Collapse
Affiliation(s)
- M.F. Galvão
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, C.P. 486, Belo Horizonte, MG 31270-901, Brazil
| | - R.W. Bastos
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, C.P. 486, Belo Horizonte, MG 31270-901, Brazil
| | - L.B. Acurcio
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, C.P. 486, Belo Horizonte, MG 31270-901, Brazil
| | - B.B. Nascimento
- Departamento de Patologia Geral, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, C.P. 486, Belo Horizonte, MG 31270-901, Brazil
| | - S.H.C. Sandes
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG 31270-901, Brazil
| | - R.M.E. Arantes
- Departamento de Patologia Geral, Universidade Federal de Minas Gerais, Avenida Antonio Carlos 6627, C.P. 486, Belo Horizonte, MG 31270-901, Brazil
| | - M.R. Souza
- Escola de Veterinária, Inspeção e Tecnologia de Produtos de Origem Animal, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG 30123-970, Brazil
| | - F.S. Martins
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, C.P. 486, Belo Horizonte, MG 31270-901, Brazil
| | - L.Q. Vieira
- Departamento de Imunologia-Bioquímica, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG 30123-970, Brazil
| | - J.R. Nicoli
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, C.P. 486, Belo Horizonte, MG 31270-901, Brazil
| |
Collapse
|
168
|
Garcia-Mazcorro JF, Barcenas-Walls JR, Suchodolski JS, Steiner JM. Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructo-oligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing. PeerJ 2017; 5:e3184. [PMID: 28439463 PMCID: PMC5398277 DOI: 10.7717/peerj.3184] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/14/2017] [Indexed: 01/18/2023] Open
Abstract
Prebiotics are selectively fermentable dietary compounds that result in changes in the composition and/or activity of the intestinal microbiota, thus conferring benefits upon host health. In veterinary medicine, commercially available products containing prebiotics have not been well studied with regard to the changes they trigger on the composition of the gut microbiota. This study evaluated the effect of a commercially available nutraceutical containing fructo-oligosaccharides (FOS) and inulin on the fecal microbiota of healthy cats and dogs when administered for 16 days. Fecal samples were collected at two time points before and at two time points during prebiotic administration. Total genomic DNA was obtained from fecal samples and 454-pyrosequencing was used for 16S rRNA gene bacterial profiling. The linear discriminant analysis (LDA) effect size (LEfSe) method was used for detecting bacterial taxa that may respond (i.e., increase or decrease in its relative abundance) to prebiotic administration. Prebiotic administration was associated with a good acceptance and no side effects (e.g., diarrhea) were reported by the owners. A low dose of prebiotics (50 mL total regardless of body weight with the end product containing 0.45% of prebiotics) revealed a lower abundance of Gammaproteobacteria and a higher abundance of Veillonellaceae during prebiotic administration in cats, while Staphylococcaceae showed a higher abundance during prebiotic administration in dogs. These differences were not sufficient to separate bacterial communities as shown by analysis of weighted UniFrac distance metrics. A predictive approach of the fecal bacterial metagenome using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) also did not reveal differences between the period before and during prebiotic administration. A second trial using a higher dose of prebiotics (3.2 mL/kg body weight with the end product containing 3.1% of prebiotics) was tested in dogs and revealed a lower abundance of Dorea (family Clostridiaceae) and a higher abundance of Megamonas and other (unknown) members of Veillonellaceae during prebiotic administration. Again, these changes were not sufficient to separate bacterial communities or predicted metabolic profiles according to treatment. A closer analysis of bacterial communities at all time-points revealed highly individualized patterns of variation. This study shows a high interindividual variation of fecal bacterial communities from pet cats and dogs, that these communities are relatively stable over time, and that some of this variation can be attributable to prebiotic administration, a phenomenon that may be affected by the amount of the prebiotic administered in the formulation. This study also provides insights into the response of gut bacterial communities in pet cats and dogs during administration of commercially available products containing prebiotics. More studies are needed to explore potentially beneficial effects on host health beyond changes in bacterial communities.
Collapse
Affiliation(s)
- Jose F Garcia-Mazcorro
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States.,Faculty of Veterinary Medicine, Universidad Autónoma de Nuevo León, General Escobedo, Nuevo Leon, Mexico
| | - Jose R Barcenas-Walls
- Center for Research and Development in Health Sciences (CIDICS), Genomics Unit, Universidad Autónoma de Nuevo León, Monterrey, Nuevo Leon, Mexico
| | - Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Jörg M Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
169
|
High-avidity IgA protects the intestine by enchaining growing bacteria. Nature 2017; 544:498-502. [PMID: 28405025 DOI: 10.1038/nature22058] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/10/2017] [Indexed: 12/22/2022]
Abstract
Vaccine-induced high-avidity IgA can protect against bacterial enteropathogens by directly neutralizing virulence factors or by poorly defined mechanisms that physically impede bacterial interactions with the gut tissues ('immune exclusion'). IgA-mediated cross-linking clumps bacteria in the gut lumen and is critical for protection against infection by non-typhoidal Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium). However, classical agglutination, which was thought to drive this process, is efficient only at high pathogen densities (≥108 non-motile bacteria per gram). In typical infections, much lower densities (100-107 colony-forming units per gram) of rapidly dividing bacteria are present in the gut lumen. Here we show that a different physical process drives formation of clumps in vivo: IgA-mediated cross-linking enchains daughter cells, preventing their separation after division, and clumping is therefore dependent on growth. Enchained growth is effective at all realistic pathogen densities, and accelerates pathogen clearance from the gut lumen. Furthermore, IgA enchains plasmid-donor and -recipient clones into separate clumps, impeding conjugative plasmid transfer in vivo. Enchained growth is therefore a mechanism by which IgA can disarm and clear potentially invasive species from the intestinal lumen without requiring high pathogen densities, inflammation or bacterial killing. Furthermore, our results reveal an untapped potential for oral vaccines in combating the spread of antimicrobial resistance.
Collapse
|
170
|
Gomez DE, Arroyo LG, Costa MC, Viel L, Weese JS. Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves. J Vet Intern Med 2017; 31:928-939. [PMID: 28390070 PMCID: PMC5435056 DOI: 10.1111/jvim.14695] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/13/2017] [Accepted: 02/21/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population-based studies of cattle have investigated how the microbiota is impacted during diarrhea. OBJECTIVES To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves. METHODS Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age-matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA). RESULTS Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate. CLINICAL RELEVANCE The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.
Collapse
Affiliation(s)
- D E Gomez
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - L G Arroyo
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - M C Costa
- Département de Biomédecine Vétérinaire, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - L Viel
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - J S Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
171
|
|
172
|
Davis LR, Bigler L, Woodhams DC. Developmental trajectories of amphibian microbiota: response to bacterial therapy depends on initial community structure. Environ Microbiol 2017; 19:1502-1517. [DOI: 10.1111/1462-2920.13707] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Leyla R. Davis
- Institute of Evolutionary Biology and Environmental Studies
| | - Laurent Bigler
- Institute of Organic Chemistry; University of Zurich; Winterthurerstrasse 190 Zurich CH-8057 Switzerland
| | - Douglas C. Woodhams
- Institute of Evolutionary Biology and Environmental Studies
- Department of Biology; University of Massachusetts Boston; 100 Morrissey Blvd. Boston MA 02125 USA
| |
Collapse
|
173
|
Stress during pregnancy alters temporal and spatial dynamics of the maternal and offspring microbiome in a sex-specific manner. Sci Rep 2017; 7:44182. [PMID: 28266645 PMCID: PMC5339804 DOI: 10.1038/srep44182] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/06/2017] [Indexed: 02/07/2023] Open
Abstract
The microbiome is a regulator of host immunity, metabolism, neurodevelopment, and behavior. During early life, bacterial communities within maternal gut and vaginal compartments can have an impact on directing these processes. Maternal stress experience during pregnancy may impact offspring development by altering the temporal and spatial dynamics of the maternal microbiome during pregnancy. To examine the hypothesis that maternal stress disrupts gut and vaginal microbial dynamics during critical prenatal and postnatal windows, we used high-resolution 16S rRNA marker gene sequencing to examine outcomes in our mouse model of early prenatal stress. Consistent with predictions, maternal fecal communities shift across pregnancy, a process that is disrupted by stress. Vaginal bacterial community structure and composition exhibit lasting disruption following stress exposure. Comparison of maternal and offspring microbiota revealed that similarities in bacterial community composition was predicted by a complex interaction between maternal body niche and offspring age and sex. Importantly, early prenatal stress influenced offspring bacterial community assembly in a temporal and sex-specific manner. Taken together, our results demonstrate that early prenatal stress may influence offspring development through converging modifications to gut microbial composition during pregnancy and transmission of dysbiotic vaginal microbiome at birth.
Collapse
|
174
|
Schultz BM, Paduro CA, Salazar GA, Salazar-Echegarai FJ, Sebastián VP, Riedel CA, Kalergis AM, Alvarez-Lobos M, Bueno SM. A Potential Role of Salmonella Infection in the Onset of Inflammatory Bowel Diseases. Front Immunol 2017; 8:191. [PMID: 28293241 PMCID: PMC5329042 DOI: 10.3389/fimmu.2017.00191] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD) includes a set of pathologies that result from a deregulated immune response that may affect any portion of the gastrointestinal tract. The most prevalent and defined forms of IBD are Crohn’s disease and ulcerative colitis. Although the etiology of IBD is not well defined, it has been suggested that environmental and genetic factors contribute to disease development and that the interaction between these two factors can trigger the pathology. Diet, medication use, vitamin D status, smoking, and bacterial infections have been proposed to influence or contribute to the onset or development of the disease in susceptible individuals. The infection with pathogenic bacteria is a key factor that can influence the development and severity of this disease. Here, we present a comprehensive review of studies performed in human and mice susceptible to IBD, which supports the notion that infection with bacterial pathogens, such as Salmonella, could promote the onset of IBD due to permanent changes in the intestinal microbiota, disruption of the epithelial barrier and alterations of the intestinal immune response after infection.
Collapse
Affiliation(s)
- Bárbara M Schultz
- Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Carolina A Paduro
- Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Geraldyne A Salazar
- Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Francisco J Salazar-Echegarai
- Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Valentina P Sebastián
- Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Claudia A Riedel
- Facultad de Ciencias Biológicas y Facultad de Medicina, Departamento de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Universidad Andrés Bello , Santiago , Chile
| | - Alexis M Kalergis
- Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile; Facultad de Medicina, Departamento de Endocrinología, Pontificia Universidad Católica de Chile, Santiago, Chile; INSERM, UMR 1064, Nantes, France
| | - Manuel Alvarez-Lobos
- Facultad de Medicina, Departamento de Gastroenterología, Pontificia Universidad Católica de Chile , Santiago , Chile
| | - Susan M Bueno
- Facultad de Ciencias Biológicas, Departamento de Genética Molecular y Microbiología, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile; INSERM, UMR 1064, Nantes, France
| |
Collapse
|
175
|
The Shift of an Intestinal "Microbiome" to a "Pathobiome" Governs the Course and Outcome of Sepsis Following Surgical Injury. Shock 2017; 45:475-82. [PMID: 26863118 DOI: 10.1097/shk.0000000000000534] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sepsis following surgical injury remains a growing and worrisome problem following both emergent and elective surgery. Although early resuscitation efforts and prompt antibiotic therapy have improved outcomes in the first 24 to 48 h, late onset sepsis is now the most common cause of death in modern intensive care units. This time shift may be, in part, a result of prolonged exposure of the host to the stressors of critical illness which, over time, erode the health promoting intestinal microbiota and allow for virulent pathogens to predominate. Colonizing pathogens can then subvert the immune system and contribute to the deterioration of the host response. Here, we posit that novel approaches integrating the molecular, ecological, and evolutionary dynamics of the evolving gut microbiome/pathobiome during critical illness are needed to understand and prevent the late onset sepsis that develops following prolonged critical illness.
Collapse
|
176
|
Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea. PLoS One 2017; 12:e0169851. [PMID: 28072880 PMCID: PMC5225014 DOI: 10.1371/journal.pone.0169851] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 12/22/2016] [Indexed: 01/19/2023] Open
Abstract
Early-life microbial exposure is of particular importance to growth, immune system development and long-lasting health. Hence, early microbiota composition is a promising predictive biomarker for health and disease but still remains poorly characterized in regards to susceptibility to diarrhoea. In the present study, we aimed to assess if gut bacterial community diversity and composition during the suckling period were associated with differences in susceptibility of pigs to post-weaning diarrhoea. Twenty piglets from 5 sows (4 piglets / litter) were weaned in poor housing conditions to challenge their susceptibility to post-weaning diarrhoea. Two weeks after weaning, 13 pigs exhibited liquid faeces during 2 or 3 days and were defined as diarrhoeic (D) pigs. The other 7 pigs did not have diarrhea during the whole post-weaning experimental periodand were defined as healthy (H) pigs. Using a molecular characterisation of fecal microbiota with CE-SSCP fingerprint, Next Generation Sequencing and qPCR, we show that D and H pigs were mainly discriminated as early as postnatal day (PND) 7, i.e. 4 weeks before post-weaning diarrhoea occurence. At PND 7 H pigs displayed a lower evenness and a higher abundance of Prevotellaceae, Lachnospiraceae, Ruminocacaceae and Lactobacillaceae compared to D pigs. The sPLS regression method indicates that these bacterial families were strongly correlated to a higher Bacteroidetes abundance observed in PND 30 H pigs one week before diarrhoea. These results emphasize the potential of early microbiota diversity and composition as being an indicator of susceptibility to post-weaning diarrhoea. Furthermore, they support the health promoting strategies of pig herds through gut microbiota engineering.
Collapse
|
177
|
Huang YJ, Erb-Downward JR, Dickson RP, Curtis JL, Huffnagle GB, Han MK. Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions. Transl Res 2017; 179:71-83. [PMID: 27392936 PMCID: PMC5164976 DOI: 10.1016/j.trsl.2016.06.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 12/23/2022]
Abstract
In the past several years, advances in sequencing platforms and bioinformatics have transformed our understanding of the relationship between microbial ecology and human health. Both the normal and diseased lung are host to hundreds of bacterial genera, blurring the lines between "colonization" and "infection". However, whereas in health the respiratory microbiome is determined primarily by the dynamic balance of immigration and elimination, in chronic disease conditions become much more favorable for the reproduction of resident bacteria. Recent studies demonstrate that the microbiota of the chronic obstructive pulmonary disease (COPD) lung differ from the healthy lung although significant intrasubject and intersubject heterogeneity are still present with variation impacted by factors such as disease stage and inhaled medications. Changes in the relative abundance of specific bacterial taxa during COPD exacerbations have also been noted although further longitudinal analyses are needed to ascertain the malleability and resilience of this ecological system and its role in the occurrence and frequency of exacerbations. Whether patients with a "frequent exacerbator" phenotype possess specific or greater alterations in their airway microbiome that predispose them to recurrent exacerbations as compared with nonfrequent exacerbators needs to be determined. Although recent data suggest that the presence of bacteria has the potential to influence the host immune response, a key challenge in the next few years will be to continue to move beyond descriptive studies to define the clinical relevance of differences in lung microbiota associated with COPD.
Collapse
Affiliation(s)
- Yvonne J Huang
- Division of Pulmonary and Critical Care, University of Michigan, Ann Arbor, Mich
| | - John R Erb-Downward
- Division of Pulmonary and Critical Care, University of Michigan, Ann Arbor, Mich
| | - Robert P Dickson
- Division of Pulmonary and Critical Care, University of Michigan, Ann Arbor, Mich
| | - Jeffrey L Curtis
- Division of Pulmonary and Critical Care, University of Michigan, Ann Arbor, Mich; Pulmonary & Critical Care Medicine Section, Medical Service, VA, Ann Arbor, Mich
| | - Gary B Huffnagle
- Division of Pulmonary and Critical Care, University of Michigan, Ann Arbor, Mich
| | - MeiLan K Han
- Division of Pulmonary and Critical Care, University of Michigan, Ann Arbor, Mich.
| |
Collapse
|
178
|
|
179
|
Kwong Chung CKC, Ronchi F, Geuking MB. Detrimental effect of systemic antimicrobial CD4 + T-cell reactivity on gut epithelial integrity. Immunology 2016; 150:221-235. [PMID: 27779311 PMCID: PMC5214769 DOI: 10.1111/imm.12682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/09/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
Healthy host-microbe mutualism relies on compartmentalization and proper regulation of systemic and mucosal immune responses. Nevertheless, the systemic immune system is frequently exposed to bouts of bacteraemia, which can trigger systemic antimicrobial immune reactivity including CD4+ T cells. Low-level bacteraemia can occur when immune compartmentalization is compromised, for example in the presence of innate immune deficiency or following use of non-steroidal anti-inflammatory drugs. We generated an Escherichia coli strain expressing a defined T helper neo-epitope to study systemic antigen-specific antimicrobial CD4+ T cells and their potential involvement in the pathogenisis of inflammatory bowel diseases. We found that the dose of bacteria required for the induction of systemic antimicrobial CD4+ T-cell proliferation was high and not easily reached under physiological conditions. Importantly, however, when intestinal barrier function was compromised by induced damage to the intestinal epithelium, the presence of systemic antimicrobial CD4+ T cells specific for a single neo-antigen resulted in dramatically increased levels of bacterial translocation. This study therefore demonstrates that systemic antimicrobial CD4+ T-cell reactivity might impact adversely on the mucosa under conditions of reduced barrier function and that despite strong mucosal immune regulation, antigen-specific recognition is still sensitive.
Collapse
Affiliation(s)
- Cheong K C Kwong Chung
- Department of Clinical Research (DKF), Mucosal Immunology Laboratory, University of Bern, Bern, Switzerland
| | - Francesca Ronchi
- Department of Clinical Research (DKF), Mucosal Immunology Laboratory, University of Bern, Bern, Switzerland
| | - Markus B Geuking
- Department of Clinical Research (DKF), Mucosal Immunology Laboratory, University of Bern, Bern, Switzerland.,Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
180
|
Gart EV, Suchodolski JS, Welsh TH, Alaniz RC, Randel RD, Lawhon SD. Salmonella Typhimurium and Multidirectional Communication in the Gut. Front Microbiol 2016; 7:1827. [PMID: 27920756 PMCID: PMC5118420 DOI: 10.3389/fmicb.2016.01827] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022] Open
Abstract
The mammalian digestive tract is home to trillions of microbes, including bacteria, archaea, protozoa, fungi, and viruses. In monogastric mammals the stomach and small intestine harbor diverse bacterial populations but are typically less populated than the colon. The gut bacterial community (microbiota hereafter) varies widely among different host species and individuals within a species. It is influenced by season of the year, age of the host, stress and disease. Ideally, the host and microbiota benefit each other. The host provides nutrients to the microbiota and the microbiota assists the host with digestion and nutrient metabolism. The resident microbiota competes with pathogens for space and nutrients and, through this competition, protects the host in a phenomenon called colonization resistance. The microbiota participates in development of the host immune system, particularly regulation of autoimmunity and mucosal immune response. The microbiota also shapes gut–brain communication and host responses to stress; and, indeed, the microbiota is a newly recognized endocrine organ within mammalian hosts. Salmonella enterica serovar Typhimurium (S. Typhimurium hereafter) is a food-borne pathogen which adapts to and alters the gastrointestinal (GI) environment. In the GI tract, S. Typhimurium competes with the microbiota for nutrients and overcomes colonization resistance to establish infection. To do this, S. Typhimurium uses multiple defense mechanisms to resist environmental stressors, like the acidic pH of the stomach, and virulence mechanisms which allow it to invade the intestinal epithelium and disseminate throughout the host. To coordinate gene expression and disrupt signaling within the microbiota and between host and microbiota, S. Typhimurium employs its own chemical signaling and may regulate host hormone metabolism. This review will discuss the multidirectional interaction between S. Typhimurium, host and microbiota as well as mechanisms that allow S. Typhimurium to succeed in the gut.
Collapse
Affiliation(s)
- Elena V Gart
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station TX, USA
| | - Jan S Suchodolski
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Texas A&M University, College Station TX, USA
| | - Thomas H Welsh
- Department of Animal Science, College of Agriculture and Life Sciences, Texas A&M University, College Station TX, USA
| | - Robert C Alaniz
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station TX, USA
| | | | - Sara D Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station TX, USA
| |
Collapse
|
181
|
Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ, Ring D, Diehl M, Herp S, Lötscher Y, Hussain S, Bunk B, Pukall R, Huson DH, Münch PC, McHardy AC, McCoy KD, Macpherson AJ, Loy A, Clavel T, Berry D, Stecher B. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol 2016; 2:16215. [PMID: 27869789 DOI: 10.1038/nmicrobiol.2016.215] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/26/2016] [Indexed: 02/07/2023]
Abstract
Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse-Microbiota (Oligo-MM12), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM12. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the mouse intestinal bacterial collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genome-guided design can be used to generate insights into microbe-microbe and microbe-host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.
Collapse
Affiliation(s)
- Sandrine Brugiroux
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
| | - Markus Beutler
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
| | - Carina Pfann
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Vienna, Austria
| | - Debora Garzetti
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
- German Center for Infection Research (DZIF); Partner Site Munich
| | | | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
| | - Manuel Diehl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
| | - Simone Herp
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
| | - Yvonne Lötscher
- Institute of Microbiology, ETH Zürich, 8093 Zürich, Switzerland
| | - Saib Hussain
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
| | - Boyke Bunk
- DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Rüdiger Pukall
- DSMZ - German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Daniel H Huson
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Philipp C Münch
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Alice C McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
- Department of Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Kathy D McCoy
- Maurice Müller Laboratories, Department of Clinical Research (DKF), UVCM, University Hospital, 3010 Bern, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department of Clinical Research (DKF), UVCM, University Hospital, 3010 Bern, Switzerland
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Vienna, Austria
| | - Thomas Clavel
- ZIEL Institute for Food and Health, Technische Universität München, 85354 Freising, Germany
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, A-1090 Vienna, Austria
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
- German Center for Infection Research (DZIF); Partner Site Munich
| |
Collapse
|
182
|
Zhu J, Dai W, Qiu Q, Dong C, Zhang J, Xiong J. Contrasting Ecological Processes and Functional Compositions Between Intestinal Bacterial Community in Healthy and Diseased Shrimp. MICROBIAL ECOLOGY 2016; 72:975-985. [PMID: 27538872 DOI: 10.1007/s00248-016-0831-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Intestinal bacterial communities play a pivotal role in promoting host health; therefore, the disruption of intestinal bacterial homeostasis could result in disease. However, the effect of the occurrences of disease on intestinal bacterial community assembly remains unclear. To address this gap, we compared the multifaceted ecological differences in maintaining intestinal bacterial community assembly between healthy and diseased shrimps. The neutral model analysis shows that the relative importance of neutral processes decreases when disease occurs. This pattern is further corroborated by the ecosphere null model, revealing that the bacterial community assembly of diseased samples is dominated by stochastic processes. In addition, the occurrence of shrimp disease reduces the complexity and cooperative activities of species-to-species interactions. The keystone taxa affiliated with Alphaproteobacteria and Actinobacteria in healthy shrimp gut shift to Gammaproteobacteria species in diseased shrimp. Changes in intestinal bacterial communities significantly alter biological functions in shrimp. Within a given metabolic pathway, the pattern of enrichment or decrease between healthy and deceased shrimp is correlated with its functional effects. We propose that stressed shrimp are more prone to invasion by alien strains (evidenced by more stochastic assembly and higher migration rate in diseased shrimp), which, in turn, disrupts the cooperative activity among resident species. These findings greatly aid our understanding of the underlying mechanisms that govern shrimp intestinal community assembly between health statuses.
Collapse
Affiliation(s)
- Jinyong Zhu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wenfang Dai
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State of Oceanic Administration, Xiamen, 361006, China
| | - Jinjie Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Jinbo Xiong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, 315211, China.
| |
Collapse
|
183
|
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) has been proposed as a therapeutic approach for functional gastrointestinal disease. We launched a clinical study to examine the safety and efficacy of FMT for slow transit constipation (STC). MATERIALS AND METHODS Twenty-four patients with STC, aged from 20 to 74 were enrolled in this prospective open-label study. Patients received FMT on 3 consecutive days through nasojejunal tubes and followed up for 12 weeks after treatment. Rate of clinical improvement and remission, Wexner constipation scale, Bowel movement per week, and gastrointestinal quality-of-life index were evaluated. RESULTS The rate of clinical improvement and remission based on clinical activity at week 12 was 50% (12/24) and 37.5% (9/24), respectively. The patient's stool frequency increased from a mean of 1.8 (SD 1.3) per week pre-FMT to 4.1 (SD 2.6) at week 12 post-FMT without laxative usage (P<0.01). The stool consistency showed a tendency to improve after FMT administration. Comparison of pre-FMT and post-FMT Wexner constipation scores demonstrated a significant reduction between baseline (14.1±3.3) and the first week (9.8±4.9), which was maintained up to the following 12 weeks (7.5±3.2; P<0.01). Compared with baseline, significant overall improvements were also seen in gastrointestinal quality-of-life index score at week 1, week 2, week 4, week 8, and week 12 of follow-up (P<0.01). The improvements were accompanied by the decline of colonic transit time. No severe adverse events during the whole FMT procedure follow-up except for venting (6/24), abdominal pain (3/24), bloating (2/24), and diarrhea (7/24). CONCLUSION This is a pilot study demonstrating that FMT was safe and may have the potential to improve symptoms in patients with STC.
Collapse
|
184
|
Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome. Cell Host Microbe 2016; 20:515-526. [DOI: 10.1016/j.chom.2016.09.001] [Citation(s) in RCA: 253] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/25/2016] [Accepted: 09/08/2016] [Indexed: 12/18/2022]
|
185
|
Erny D, Hrabě de Angelis AL, Prinz M. Communicating systems in the body: how microbiota and microglia cooperate. Immunology 2016; 150:7-15. [PMID: 27392533 DOI: 10.1111/imm.12645] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 06/25/2016] [Accepted: 06/28/2016] [Indexed: 12/11/2022] Open
Abstract
Microglia are tissue macrophages of the central nervous system (CNS). Their key tasks are immune surveillance as well as responding to infections or other pathological states such as neurological diseases or injury. In recent years it has been discovered that microglia are additionally crucial for the maintenance of brain homeostasis during development and adulthood by adjusting the neuronal network and phagocytosing neuronal debris. Microglia persist in the CNS throughout the life of the organism and self-renew without engraftment of bone-marrow-derived cells. Until recently it remained unknown what controls their maturation and activation under homeostatic conditions. In this review we discuss new aspects of the interaction between host microbiota and brain function with special focus on the brain-resident innate immune cells, the microglia.
Collapse
Affiliation(s)
- Daniel Erny
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| |
Collapse
|
186
|
Paganini D, Uyoga MA, Zimmermann MB. Iron Fortification of Foods for Infants and Children in Low-Income Countries: Effects on the Gut Microbiome, Gut Inflammation, and Diarrhea. Nutrients 2016; 8:nu8080494. [PMID: 27529276 PMCID: PMC4997407 DOI: 10.3390/nu8080494] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 07/25/2016] [Accepted: 08/01/2016] [Indexed: 12/19/2022] Open
Abstract
Iron deficiency anemia (IDA) is common among infants and children in Sub-Saharan Africa and is a leading contributor to the global burden of disease, as well as a hindrance to national development. In-home iron fortification of complementary foods using micronutrient powders (MNPs) effectively reduces the risk for IDA by ensuring that the iron needs of infants and young children are met without changing their traditional diet. However, the iron dose delivered by MNPs is high, and comparable on a mg iron per kg body weight to the supplemental doses (2 mg/kg) typically given to older children, which increases diarrhea risk. In controlled studies, iron-containing MNPs modestly increase risk for diarrhea in infants; in some cases, the diarrhea is severe and may require hospitalization. Recent in vitro and in vivo studies provide insights into the mechanism of this effect. Provision of iron fortificants to school-age children and iron-containing MNPs to weaning infants decreases the number of beneficial ‘barrier’ commensal gut bacteria (e.g., bifidobacteria), increases the enterobacteria to bifidobacteria ratio and abundances of opportunistic pathogens (e.g., pathogenic Escherichia coli), and induces gut inflammation. Thus, although iron-containing MNPs are highly effective in reducing IDA, they may increase gastrointestinal morbidity in infants, and safer formulations are needed.
Collapse
Affiliation(s)
- Daniela Paganini
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, ETH Zurich, Zurich 8092, Switzerland.
| | - Mary A Uyoga
- College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.
| | - Michael B Zimmermann
- Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, ETH Zurich, Zurich 8092, Switzerland.
| |
Collapse
|
187
|
Abstract
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
Collapse
Affiliation(s)
- Deirdre L Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada T2N 1N4
| |
Collapse
|
188
|
Nutrient Deprivation Affects Salmonella Invasion and Its Interaction with the Gastrointestinal Microbiota. PLoS One 2016; 11:e0159676. [PMID: 27437699 PMCID: PMC4954642 DOI: 10.1371/journal.pone.0159676] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/06/2016] [Indexed: 01/30/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a foodborne enteric pathogen and a major cause of gastroenteritis in humans. It is known that molecules derived from the human fecal microbiota downregulate S. Typhimurium virulence gene expression and induce a starvation-like response. In this study, S. Typhimurium was cultured in minimal media to mimic starvation conditions such as that experienced by S. Typhimurium in the human intestinal tract, and the pathogen’s virulence in vitro and in vivo was measured. S. Typhimurium cultured in minimal media displayed a reduced ability to invade human epithelial cells in a manner that was at least partially independent of the Salmonella Pathogenicity Island 1 (SPI-1) type III secretion system. Nutrient deprivation did not, however, alter the ability of S. Typhimurium to replicate and survive inside epithelial cells. In a murine model of S. Typhimurium-induced gastroenteritis, prior cultivation in minimal media did not alter the pathogen’s ability to colonize mice, nor did it affect levels of gastrointestinal inflammation. Upon examining the post-infection fecal gastrointestinal microbiota, we found that specifically in the 129Sv/ImJ murine strain S. Typhimurium cultured in minimal media induced differential microbiota compositional shifts compared to that of S. Typhimurium cultured in rich media. Together these findings demonstrate that S. Typhimurium remains a potent pathogen even in the face of nutritional deprivation, but nevertheless that nutrient deprivation encountered in this environment elicits significant changes in the bacterium genetic programme, as well as its capacity to alter host microbiota composition.
Collapse
|
189
|
McKenney ES, Kendall MM. Microbiota and pathogen 'pas de deux': setting up and breaking down barriers to intestinal infection. Pathog Dis 2016; 74:ftw051. [PMID: 27252177 PMCID: PMC5985477 DOI: 10.1093/femspd/ftw051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/04/2016] [Accepted: 05/24/2016] [Indexed: 02/07/2023] Open
Abstract
The gut microbiota plays essential roles in human health and disease. In this review, we focus on the role of the intestinal microbiota in promoting resistance to infection by bacterial pathogens as well as how pathogens overcome this barrier. We discuss how the resident microbiota restricts growth and colonization of invading pathogens by limiting availability of nutrients and through generation of a hostile environment. Additionally, we examine how microbiota-derived signaling molecules interfere with bacterial virulence. In turn, we discuss how pathogens exploit non-competitive metabolites to replicate in vivo as well as to precisely control virulence and cause disease. This bacterial two step of creating and overcoming challenges important in preventing and establishing infection highlights the complexities of elucidating interactions between the commensal bacteria and pathogens. Better understanding of microbiota-pathogen interplay will have significant implications for developing novel therapeutics to treat infectious diseases.
Collapse
Affiliation(s)
- Elizabeth S McKenney
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Melissa M Kendall
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| |
Collapse
|
190
|
Wymore Brand M, Wannemuehler MJ, Phillips GJ, Proctor A, Overstreet AM, Jergens AE, Orcutt RP, Fox JG. The Altered Schaedler Flora: Continued Applications of a Defined Murine Microbial Community. ILAR J 2016; 56:169-78. [PMID: 26323627 DOI: 10.1093/ilar/ilv012] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gastrointestinal (GI) microbiota forms a mutualistic relationship with the host through complex and dynamic interactions. Because of the complexity and interindividual variation of the GI microbiota, investigating how members of the microbiota interact with each other, as well as with the host, is daunting. The altered Schaedler flora (ASF) is a model community of eight microorganisms that was developed by R.P. Orcutt and has been in use since the late 1970s. The eight microorganisms composing the ASF were all derived from mice, can be cultured in vitro, and are stably passed through multiple generations (at least 15 years or more by the authors) in gnotobiotic mice continually bred in isolator facilities. With the limitations associated with conventional, mono- or biassociated, and germfree mice, use of mice colonized with a consortium of known bacteria that naturally inhabit the murine gut offers a powerful system to investigate mechanisms governing host-microbiota relationships, and how members of the GI microbiota interact with one another. The ASF community offers significant advantages to study homeostatic as well as disease-related interactions by taking advantage of a well-defined, limited community of microorganisms. For example, quantification and spatial distribution of individual members, microbial genetic manipulation, genomic-scale analysis, and identification of microorganism-specific host immune responses are all achievable using the ASF model. This review compiles highlights associated with the 37-year history of the ASF, including descriptions of its continued use in biomedical research to elucidate the complexities of host-microbiome interactions in health and disease.
Collapse
Affiliation(s)
- Meghan Wymore Brand
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| | - Michael J Wannemuehler
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| | - Gregory J Phillips
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| | - Alexandra Proctor
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| | - Anne-Marie Overstreet
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| | - Albert E Jergens
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| | - Roger P Orcutt
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| | - James G Fox
- Meghan Wymore Brand, DVM, is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Michael J. Wannemuehler, MS, PhD, is Professor and Chair in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Gregory J. Phillips, MA, PhD, is a professor in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Alexandra Proctor is a graduate student in the Department of Veterinary Microbiology and Preventive Medicine at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Anne-Marie Overstreet, PhD, is a postdoctoral fellow in the Department of Microbiology and Immunology at Indiana University School of Medicine-South Bend in South Bend, Indiana. Albert E. Jergens, DVM, MS, PhD, is Professor and Associate Chair for Research and Graduate Studies in the Department of Veterinary Clinical Sciences at the College of Veterinary Medicine at Iowa State University in Ames, Iowa. Roger P. Orcutt, PhD, is a consultant at Biomedical Research Associates in Dunkirk, New York. James G. Fox, MS, DVM, is Director of the Division of Comparative Medicine and Professor in the Department of Biological Engineering at Massachusetts Institute of Technology in Cambridge, Massachusetts
| |
Collapse
|
191
|
A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. Nat Commun 2016; 7:11939. [PMID: 27340092 PMCID: PMC4931012 DOI: 10.1038/ncomms11939] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/13/2016] [Indexed: 12/29/2022] Open
Abstract
Recent studies have demonstrated that gut microbiota development influences infants' health and subsequent host physiology. However, the factors shaping the development of the microbiota remain poorly understood, and the mechanisms through which these factors affect gut metabolite profiles have not been extensively investigated. Here we analyse gut microbiota development of 27 infants during the first month of life. We find three distinct clusters that transition towards Bifidobacteriaceae-dominant microbiota. We observe considerable differences in human milk oligosaccharide utilization among infant bifidobacteria. Colonization of fucosyllactose (FL)-utilizing bifidobacteria is associated with altered metabolite profiles and microbiota compositions, which have been previously shown to affect infant health. Genome analysis of infants' bifidobacteria reveals an ABC transporter as a key genetic factor for FL utilization. Thus, the ability of bifidobacteria to utilize FL and the presence of FL in breast milk may affect the development of the gut microbiota in infants, and might ultimately have therapeutic implications. The factors shaping the development of infants' gut microbiota are poorly understood. Here, the authors show that alterations in gut microbiota development in infants are associated with the presence of bifidobacteria having a gene for utilisation of human milk oligosaccharides.
Collapse
|
192
|
Advances, challenges, and directions in shrimp disease control: the guidelines from an ecological perspective. Appl Microbiol Biotechnol 2016; 100:6947-54. [PMID: 27333908 DOI: 10.1007/s00253-016-7679-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/07/2016] [Accepted: 06/11/2016] [Indexed: 12/23/2022]
Abstract
High-density aquaculture has led to increasing occurrences of diseases in shrimp. Thus, it is imperative to establish effective and quantitative strategies for preventing and predicting these diseases. Water quality indices and investigations of specific pathogen abundance provide only a qualitative evaluation of the risk of shrimp disease and can be inaccurate. To address these shortcomings, we introduced intestinal indicative assemblages as independent variables with which to quantitatively predict incidences of shrimp disease. Given the ignorance regarding the niches differences in the shrimp intestine throughout its developmental stages, the use of probiotics in aquaculture has had limited success. Therefore, we propose the exploration of effective probiotic bacteria from shrimp intestinal flora and the establishment of therapeutic strategies dependent on shrimp age. Following ecological selection principles, we hypothesize that the larval stage provides the best opportunity to establish a desired gut microbiota through preemptive colonization of the treated rearing water with known probiotics. To employ this strategy, however, substantial barriers must be overcome.
Collapse
|
193
|
Krezalek MA, Skowron KB, Guyton KL, Shakhsheer B, Hyoju S, Alverdy JC. The intestinal microbiome and surgical disease. Curr Probl Surg 2016; 53:257-93. [PMID: 27497246 DOI: 10.1067/j.cpsurg.2016.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/07/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Monika A Krezalek
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Kinga B Skowron
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Kristina L Guyton
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Baddr Shakhsheer
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Sanjiv Hyoju
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - John C Alverdy
- Department of Surgery, Center for Surgical Infection Research and Therapeutics, Pritzker School of Medicine, University of Chicago, Chicago, IL.
| |
Collapse
|
194
|
Ktsoyan ZA, Mkrtchyan MS, Zakharyan MK, Mnatsakanyan AA, Arakelova KA, Gevorgyan ZU, Sedrakyan AM, Hovhannisyan AI, Arakelyan AA, Aminov RI. Systemic Concentrations of Short Chain Fatty Acids Are Elevated in Salmonellosis and Exacerbation of Familial Mediterranean Fever. Front Microbiol 2016; 7:776. [PMID: 27252692 PMCID: PMC4877380 DOI: 10.3389/fmicb.2016.00776] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022] Open
Abstract
Gut microbiota-produced short chain fatty acids (SCFAs) play an important role in the normal human metabolism and physiology. Although the gradients of SCFAs from the large intestine, where they are largely produced, to the peripheral blood as well as the main routes of SCFA metabolism by different organs are known well for the healthy state, there is a paucity of information regarding how these are affected in disease. In particular, how the inflammation caused by infection or autoinflammatory disease affect the concentration of SCFAs in the peripheral venous blood. In this work, we revealed that diseases caused either by infectious agents (two Salmonella enterica serovars, S. Enteritidis, and S. Typhimurium) or by the exacerbation of an autoinflammatory disease, familial Mediterranean fever (FMF), both result in a significantly elevated systemic concentration of SCFAs. In the case of salmonellosis the concentration of SCFAs in peripheral blood was significantly and consistently higher, from 5- to 20-fold, compared to control. In the case of FMF, however, a significant increase of SCFAs in the peripheral venous blood was detected only in the acute phase of the disease, with a lesser impact in remission. It seems counterintuitive that the dysbiotic conditions, with a reduced number of gut microorganisms, produce such an effect. This phenomenon, however, must be appraised within the context of how the inflammatory diseases affect the normal physiology. We discuss a number of factors that may contribute to the “leak” and persistence of gut-produced SCFAs into the systemic circulation in infectious and autoinflammatory diseases.
Collapse
Affiliation(s)
- Zhanna A Ktsoyan
- Institute of Molecular Biology of National Academy of Sciences of Republic of Armenia Yerevan, Armenia
| | - Mkhitar S Mkrtchyan
- Institute of Molecular Biology of National Academy of Sciences of Republic of Armenia Yerevan, Armenia
| | - Magdalina K Zakharyan
- Institute of Molecular Biology of National Academy of Sciences of Republic of Armenia Yerevan, Armenia
| | - Armine A Mnatsakanyan
- Clinical Hospital of Infectious Diseases Nork, Ministry of Health of Republic of Armenia Yerevan, Armenia
| | - Karine A Arakelova
- Institute of Molecular Biology of National Academy of Sciences of Republic of Armenia Yerevan, Armenia
| | - Zaruhi U Gevorgyan
- Clinical Hospital of Infectious Diseases Nork, Ministry of Health of Republic of Armenia Yerevan, Armenia
| | - Anahit M Sedrakyan
- Institute of Molecular Biology of National Academy of Sciences of Republic of Armenia Yerevan, Armenia
| | - Alvard I Hovhannisyan
- Institute of Molecular Biology of National Academy of Sciences of Republic of Armenia Yerevan, Armenia
| | - Arsen A Arakelyan
- Institute of Molecular Biology of National Academy of Sciences of Republic of Armenia Yerevan, Armenia
| | - Rustam I Aminov
- School of Medicine and Dentistry, University of Aberdeen Aberdeen, UK
| |
Collapse
|
195
|
Munyaka PM, Rabbi MF, Khafipour E, Ghia JE. Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice. J Basic Microbiol 2016; 56:986-98. [PMID: 27112251 DOI: 10.1002/jobm.201500726] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/18/2016] [Indexed: 12/20/2022]
Abstract
UNLABELLED The most widely used and characterized experimental model of ulcerative colitis (UC) is the epithelial erosion, dextran sulfate sodium (DSS)-induced colitis, which is developed by administration of DSS in drinking water. We investigated fecal and colonic mucosa microbial composition and functional changes in mice treated with DSS. C57Bl/6 mice received 5% DSS in drinking water for 5 days. Inflammation was evaluated clinically and by analysis of colonic tissue cytokine levels and C-reactive protein (CRP) in the serum. Colonic mucosa and fecal samples were used for DNA extraction and the V4 region of bacterial 16S rRNA gene was subjected to MiSeq Illumina sequencing. Alpha- and beta-diversities, and compositional differences at phylum and genus levels were determined, and bacterial functional pathways were predicted. DSS increased disease severity, serum CRP and cytokines IL-1β and IL-6, but decreased bacterial species richness, and shifted bacterial community composition. Bacteroides, Turicibacter, Escherichia, Clostridium, Enterobacteriaceae, Clostridiaceae, Bacteroidaceae, Bacteroidales, among other taxa were associated with DSS treatment in fecal and colonic samples. Also, DSS altered microbial functional pathways in both colonic mucosa and fecal samples. CONCLUSIONS The development of colitis in DSS model was accompanied with reduced microbial diversity and dysbiosis of gut microbiota at lower taxonomical levels.
Collapse
Affiliation(s)
- Peris Mumbi Munyaka
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, Manitoba, Canada. .,Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Jean-Eric Ghia
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada. .,Department of Internal Medicine, Section of Gastroenterology, University of Manitoba, Winnipeg, Manitoba, Canada. .,Inflammatory Bowel Disease Clinical & Research Centre, University of Manitoba, Winnipeg, Manitoba, Canada.
| |
Collapse
|
196
|
The Roles of Inflammation, Nutrient Availability and the Commensal Microbiota in Enteric Pathogen Infection. Microbiol Spectr 2016; 3. [PMID: 26185088 DOI: 10.1128/microbiolspec.mbp-0008-2014] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The healthy human intestine is colonized by as many as 1014 bacteria belonging to more than 500 different species forming a microbial ecosystem of unsurpassed diversity, termed the microbiota. The microbiota's various bacterial members engage in a physiological network of cooperation and competition within several layers of complexity. Within the last 10 years, technological progress in the field of next-generation sequencing technologies has tremendously advanced our understanding of the wide variety of physiological and pathological processes that are influenced by the commensal microbiota (1, 2). An increasing number of human disease conditions, such as inflammatory bowel diseases (IBD), type 2 diabetes, obesity, allergies and colorectal cancer are linked with altered microbiota composition (3). Moreover, a clearer picture is emerging of the composition of the human microbiota in healthy individuals, its variability over time and between different persons and how the microbiota is shaped by environmental factors (i.e., diet) and the host's genetic background (4). A general feature of a normal, healthy gut microbiota can generate conditions in the gut that disfavor colonization of enteric pathogens. This is termed colonization-resistance (CR). Upon disturbance of the microbiota, CR can be transiently disrupted, and pathogens can gain the opportunity to grow to high levels. This disruption can be caused by exposure to antibiotics (5, 6), changes in diet (7, 8), application of probiotics and drugs (9), and a variety of diseases (3). Breakdown of CR can boost colonization by intrinsic pathogens or increase susceptibility to infections (10). One consequence of pathogen expansion is the triggering of inflammatory host responses and pathogen-mediated disease. Interestingly, human enteric pathogens are part of a small group of bacterial families that belong to the Proteobacteria: the Enterobacteriaceae (E. coli, Yersinia spp., Salmonella spp., Shigella spp.), the Vibrionaceae (Vibrio cholerae) and the Campylobacteriaceae (Campylobacter spp.). In general, members of these families (be it commensals or pathogens) only constitute a minority of the intestinal microbiota. However, proteobacterial "blooms" are a characteristic trait of an abnormal microbiota such as in the course of antibiotic therapy, dietary changes or inflammation (11). It has become clear that the gut microbiota not only plays a major role in priming and regulating mucosal and systemic immunity, but that the immune system also contributes to host control over microbiota composition. These two ways of mutual communication between the microbiota and the immune system were coined as "outside-in" and "inside-out," respectively (12). The significance of those interactions for human health is particularly evident in Crohn's disease (CD) and Ulcerative Colitis (UC). The symptoms of these recurrent, chronic types of gut inflammation are caused by an excessive immune response against one's own commensal microbiota (13). It is assumed that deregulated immune responses can be caused by a genetic predisposition, leading to, for example, the impairment of intestinal barrier function or disruption of mucosal T-cell homeostasis. In CD or UC patients, an abnormally composed microbiota, referred to as "dysbiosis," is commonly observed (discussed later). This is often characterized by an increased relative abundance of facultative anaerobic bacteria (e.g., Enterobacteriaeceae, Bacilli) and, at the same time, depletion of obligate anaerobic bacteria of the classes Bacteroidia and Clostridia. So far, it is unclear whether dysbiosis is a cause or a consequence of inflammatory bowel disease (IBD). In fact, both scenarios are equally conceivable. Recent work suggests that inflammatory immune responses in the gut (both IBD and pathogen-induced) can alter the gut luminal milieu in a way that favors dysbiosis (14). In this chapter, I present a survey on our current state of understanding of the characteristics and mechanisms underlying gut inflammation-associated dysbiosis. The role of dysbiosis in enteric infections and human IBD is discussed. In addition, I will focus on competition of enteric pathogens and the gut microbiota in the inflamed gut and the role of dysbiotic microbiota alterations (e.g., "Enterobacterial blooms" (11)) for the evolution of pathogenicity.
Collapse
|
197
|
From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease. Cell 2016; 163:1326-32. [PMID: 26638069 DOI: 10.1016/j.cell.2015.11.032] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/12/2022]
Abstract
One of the clearest functions of the gut microbiota in humans is resistance to colonization by enteric bacterial pathogens. Reconstitution of the microbiota offers an exciting therapeutic approach, but great challenges must be overcome.
Collapse
|
198
|
McLoughlin K, Schluter J, Rakoff-Nahoum S, Smith A, Foster K. Host Selection of Microbiota via Differential Adhesion. Cell Host Microbe 2016; 19:550-9. [DOI: 10.1016/j.chom.2016.02.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/26/2016] [Accepted: 02/29/2016] [Indexed: 12/16/2022]
|
199
|
Zhang C, Derrien M, Levenez F, Brazeilles R, Ballal SA, Kim J, Degivry MC, Quéré G, Garault P, van Hylckama Vlieg JET, Garrett WS, Doré J, Veiga P. Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME JOURNAL 2016; 10:2235-45. [PMID: 26953599 PMCID: PMC4989305 DOI: 10.1038/ismej.2016.13] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/18/2016] [Accepted: 01/08/2016] [Indexed: 01/01/2023]
Abstract
Resident gut microbes co-exist with transient bacteria to form the gut microbiota. Despite increasing evidence suggesting a role for transient microbes on gut microbiota function, the interplay between resident and transient members of this microbial community is poorly defined. We aimed to determine the extent to which a host's autochthonous gut microbiota influences niche permissivity to transient bacteria using a fermented milk product (FMP) as a vehicle for five food-borne bacterial strains. Using conventional and gnotobiotic rats and gut microbiome analyses (16S rRNA genes pyrosequencing and reverse transcription qPCR), we demonstrated that the clearance kinetics of one FMP bacterium, Lactococcus lactis CNCM I-1631, were dependent on the structure of the resident gut microbiota. Susceptibility of the resident gut microbiota to modulation by FMP intervention correlated with increased persistence of L. lactis. We also observed gut microbiome configurations that were associated with altered stability upon exposure to transient bacteria. Our study supports the concept that allochthonous bacteria have transient and subject-specific effects on the gut microbiome that can be leveraged to re-engineer the gut microbiome and improve dysbiosis-related diseases.
Collapse
Affiliation(s)
- Chenhong Zhang
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Muriel Derrien
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | | | - Sonia A Ballal
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jason Kim
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Gaëlle Quéré
- Life Science, Danone Nutricia Research, Palaiseau, France
| | - Peggy Garault
- Life Science, Danone Nutricia Research, Palaiseau, France
| | | | | | - Joël Doré
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - Patrick Veiga
- Life Science, Danone Nutricia Research, Palaiseau, France.,Harvard T. H. Chan School of Public Health, Boston, MA, USA
| |
Collapse
|
200
|
Bjerg AT, Sørensen MB, Krych L, Hansen LH, Astrup A, Kristensen M, Nielsen DS. The effect of Lactobacillus paracasei subsp. paracasei L. casei W8® on blood levels of triacylglycerol is independent of colonisation. Benef Microbes 2016; 6:263-9. [PMID: 25273547 DOI: 10.3920/bm2014.0033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Gut microbiota (GM) dysbiosis has been linked to obesity and its metabolic complications such as cardiovascular disease (CVD). The risk of developing CVD increases with elevated concentration of serum triacylglycerol (TAG). In a blinded, randomised two-arm parallel human intervention study we have previously found that four weeks of supplementation with Lactobacillus paracasei subsp. paracasei L. casei W8® (L. casei W8) compared to placebo reduced the concentration of TAG in 64 young healthy adults, an effect, likely mediated by a decreased stearoyl- CoA desaturase-1 (SCD1) activity. In the present study we analysed faecal samples obtained during the intervention study to investigate whether this effect was related to the ability of L. casei W8 to colonise the human gut after supplementation of L. casei W8 (1010 cfu daily) as determined by qPCR specific for L. paracasei and L. casei (L. casei group); whether L. casei W8 consumption affected GM composition as determined by 16S rRNA gene targeted 454/FLX amplicon sequencing; and whether these changes were associated with changes in TAG concentration and SCD1 activity. Faecal samples were collected at baseline, after four weeks supplementation and two weeks after the supplementation was ended, and fasting blood samples were collected at baseline and after 4 weeks. Four weeks supplementation with L. casei W8 did not affect the overall composition of the GM; however, an increase in the relative abundance of the L. casei group from 8.48×10-6% of the total GM compared to 2.83×10-3% at baseline (P<0.001) was observed. Two weeks after supplementation ended, the relative abundance of the L. casei group was still increased 14 times compared to before the intervention (P<0.01). However, neither the increase in the abundance of the L. casei group nor overall GM composition correlated with changes in blood lipids or SCD1 activity.
Collapse
Affiliation(s)
- A T Bjerg
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Nørre Alle 51, 2200 Copenhagen N, Denmark
| | - M B Sørensen
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark
| | - L Krych
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark
| | - L H Hansen
- Department of Biology, Faculty of Science, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - A Astrup
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Nørre Alle 51, 2200 Copenhagen N, Denmark
| | - M Kristensen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Nørre Alle 51, 2200 Copenhagen N, Denmark
| | - D S Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark
| |
Collapse
|