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Yuan Y, Zhao G, Ji H, Peng B, Huang Z, Jin W, Chen X, Guan H, Tang G, Zhang H, Jiang Z. Changes in the gut microbiota during and after commercial helium–oxygen saturation diving in China. Occup Environ Med 2019; 76:801-807. [DOI: 10.1136/oemed-2019-106031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
ObjectivesThe influence of commercial helium–oxygen saturation diving on divers’ gut microbiotas was assessed to provide dietary suggestion.MethodsFaecal samples of 47 divers working offshore were collected before (T1), during (T2) and after (T3) saturation diving. Their living and excursion depths were 55–134 metres underwater with a saturation duration of 12–31 days and PaO2 of 38–65 kPa. The faecal samples were examined through 16S ribosomal DNA amplicon sequencing based on the Illumina sequencing platform to analyse changes in the bacteria composition in the divers’ guts.ResultsAlthough the α and β diversity of the gut microbiota did not change significantly, we found that living in a hyperbaric environment of helium–oxygen saturation decreased the abundance of the genus Bifidobacterium, an obligate anaerobe, from 2.43%±3.83% at T1 to 0.79%±1.23% at T2 and 0.59%±0.79% at T3. Additionally, the abundance of some short-chain fatty acid (SCFA)-producing bacteria, such as Fusicatenibacter, Faecalibacterium, rectale group and Anaerostipes, showed a decreased trend in the order of before, during and after diving. On the contrary, the abundance of species, such as Lactococcus garvieae, Actinomyces odontolyticus, Peptoclostridium difficile, Butyricimonas virosa, Streptococcus mutans, Porphyromonas asaccharolytica and A. graevenitzii, showed an increasing trend, but most of them were pathogens.ConclusionsOccupational exposure to high pressure in a helium–oxygen saturation environment decreased the abundance of Bifidobacterium and some SCFA-producing bacteria, and increased the risk of pathogenic bacterial infection. Supplementation of the diver diet with probiotics or prebiotics during saturation diving might prevent these undesirable changes.
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Ingham AC, Kielsen K, Cilieborg MS, Lund O, Holmes S, Aarestrup FM, Müller KG, Pamp SJ. Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation. MICROBIOME 2019; 7:131. [PMID: 31519210 PMCID: PMC6744702 DOI: 10.1186/s40168-019-0745-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/29/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the patients' immune system with that of a foreign donor. HSCT is employed as curative immunotherapy for a number of non-malignant and malignant hematologic conditions, including cancers such as acute lymphoblastic leukemia. The procedure can be accompanied by severe side effects such as infections, acute graft-versus-host disease (aGvHD), and death. Here, we performed a longitudinal analysis of immunological markers, immune reconstitution and gut microbiota composition in relation to clinical outcomes in children undergoing HSCT. Such an analysis could reveal biomarkers, e.g., at the time point prior to HSCT, that in the future could be used to predict which patients are of high risk in relation to side effects and clinical outcomes and guide treatment strategies accordingly. RESULTS In two multivariate analyses (sparse partial least squares regression and canonical correspondence analysis), we identified three consistent clusters: (1) high concentrations of the antimicrobial peptide human beta-defensin 2 (hBD2) prior to the transplantation in patients with high abundances of Lactobacillaceae, who later developed moderate or severe aGvHD and exhibited high mortality. (2) Rapid reconstitution of NK and B cells in patients with high abundances of obligate anaerobes such as Ruminococcaceae, who developed no or mild aGvHD and exhibited low mortality. (3) High inflammation, indicated by high levels of C-reactive protein, in patients with high abundances of facultative anaerobic bacteria such as Enterobacteriaceae. Furthermore, we observed that antibiotic treatment influenced the bacterial community state. CONCLUSIONS We identify multivariate associations between specific microbial taxa, host immune markers, immune cell reconstitution, and clinical outcomes in relation to HSCT. Our findings encourage further investigations into establishing longitudinal surveillance of the intestinal microbiome and relevant immune markers, such as hBD2, in HSCT patients. Profiling of the microbiome may prove useful as a prognostic tool that could help identify patients at risk of poor immune reconstitution and adverse outcomes, such as aGvHD and death, upon HSCT, providing actionable information in guiding precision medicine.
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Affiliation(s)
- Anna Cäcilia Ingham
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Katrine Kielsen
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Malene Skovsted Cilieborg
- Comparative Pediatrics and Nutrition, Department of Clinical Veterinary and Animal Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, USA
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Klaus Gottlob Müller
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark.
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Complex Responses to Hydrogen Peroxide and Hypochlorous Acid by the Probiotic Bacterium Lactobacillus reuteri. mSystems 2019; 4:4/5/e00453-19. [PMID: 31481604 PMCID: PMC6722424 DOI: 10.1128/msystems.00453-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inflammatory diseases of the gut are associated with increased intestinal oxygen concentrations and high levels of inflammatory oxidants, including hydrogen peroxide (H2O2) and hypochlorous acid (HOCl), which are antimicrobial compounds produced by the innate immune system. This contributes to dysbiotic changes in the gut microbiome, including increased populations of proinflammatory enterobacteria (Escherichia coli and related species) and decreased levels of health-associated anaerobic Firmicutes and Bacteroidetes The pathways for H2O2 and HOCl resistance in E. coli have been well studied, but little is known about how commensal and probiotic bacteria respond to inflammatory oxidants. In this work, we have characterized the transcriptomic response of the anti-inflammatory, gut-colonizing Gram-positive probiotic Lactobacillus reuteri to both H2O2 and HOCl. L. reuteri mounts distinct but overlapping responses to each of these stressors, and both gene expression and survival were strongly affected by the presence or absence of oxygen. Oxidative stress response in L. reuteri required several factors not found in enterobacteria, including the small heat shock protein Lo18, polyphosphate kinase 2, and RsiR, an L. reuteri-specific regulator of anti-inflammatory mechanisms.IMPORTANCE Reactive oxidants, including hydrogen peroxide and hypochlorous acid, are antimicrobial compounds produced by the immune system during inflammation. Little is known, however, about how many important types of bacteria present in the human microbiome respond to these oxidants, especially commensal and other health-associated species. We have now mapped the stress response to both H2O2 and HOCl in the intestinal lactic acid bacterium Lactobacillus reuteri.
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154
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Lu Z, Imlay JA. A conserved motif liganding the [4Fe-4S] cluster in [4Fe-4S] fumarases prevents irreversible inactivation of the enzyme during hydrogen peroxide stress. Redox Biol 2019; 26:101296. [PMID: 31465957 PMCID: PMC6831887 DOI: 10.1016/j.redox.2019.101296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 11/16/2022] Open
Abstract
Organisms have evolved two different classes of the ubiquitous enzyme fumarase: the [4Fe–4S] cluster-containing class I enzymes are oxidant-sensitive, whereas the class II enzymes are iron-free and therefore oxidant-resistant. When hydrogen peroxide (H2O2) attacks the most-studied [4Fe–4S] fumarases, only the cluster is damaged, and thus the cell can rapidly repair the enzyme. However, this study shows that when elevated levels of H2O2 oxidized the class I fumarase of the obligate anaerobe Bacteroides thetaiotaomicron (Bt-Fum), a hydroxyl-like radical species was produced that caused irreversible covalent damage to the polypeptide. Unlike the fumarase of oxygen-tolerant bacteria, Bt-Fum lacks a key cysteine residue in the typical “CXnCX2C″ motif that ligands [4Fe–4S] clusters. Consequently H2O2 can access and oxidize an iron atom other than the catalytic one in its cluster. Phylogenetic analysis showed that certain clades of bacteria may have evolved the full “CXnCX2C″ motif to shield the [4Fe–4S] cluster of fumarase. This effect was reproduced by the construction of a chimeric enzyme. These data demonstrate the irreversible oxidation of Fe–S cluster enzymes and may recapitulate evolutionary steps that occurred when microorganisms originally confronted oxidizing environments. It is also suggested that, if H2O2 is generated within the colon as a consequence of inflammation or the action of lactic acid bacteria, the inactivation of fumarase could potentially impair the central fermentation pathway of Bacteroides species and contribute to gut dysbiosis.
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Affiliation(s)
- Zheng Lu
- Department of Biology, Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Shantou University, Shantou, 515063, China.
| | - James A Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave., Urbana, IL, 61801, USA
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155
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Current understanding of the gut microbiota shaping mechanisms. J Biomed Sci 2019; 26:59. [PMID: 31434568 PMCID: PMC6702754 DOI: 10.1186/s12929-019-0554-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/14/2019] [Indexed: 12/14/2022] Open
Abstract
Increasing evidences have shown strong associations between gut microbiota and many human diseases, and understanding the dynamic crosstalks of host-microbe interaction in the gut has become necessary for the detection, prevention, or therapy of diseases. Many reports have showed that diet, nutrient, pharmacologic factors and many other stimuli play dominant roles in the modulation of gut microbial compositions. However, it is inappropriate to neglect the impact of host factors on shaping the gut microbiota. In this review, we highlighted the current findings of the host factors that could modulate the gut microbiota. Particularly the epithelium-associated factors, including the innate immune sensors, anti-microbial peptides, mucus barrier, secretory IgAs, epithelial microvilli, epithelial tight junctions, epithelium metabolism, oxygen barrier, and even the microRNAs are discussed in the context of the microbiota shaping. With these shaping factors, the gut epithelial cells could select the residing microbes and affect the microbial composition. This knowledge not only could provide the opportunities to better control many diseases, but may also be used for predicting the success of fecal microbiota transplantation clinically.
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156
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Abstract
Intestinal dysbiosis is associated with a large number of disease processes including necrotizing enterocolitis and late-onset sepsis in preterm infants and colic and antibiotic-associated diarrhea in term infants. Probiotic microbes are increasingly administered to infants with the intent of decreasing risk of these acute diseases as well as chronic diseases of childhood such as asthma and atopic disease. The mechanisms by which probiotics decrease inflammation, decrease intestinal permeability, alter the intestinal microbiota, and influence metabolism have been discovered through both in vitro studies and in vivo in animal models. We review key mechanisms by which probiotic microbes improve health with emphasis on recent discoveries in the field.
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157
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The σBsignalling activation pathway in the enteropathogenClostridioides difficile. Environ Microbiol 2019; 21:2852-2870. [DOI: 10.1111/1462-2920.14642] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 01/05/2023]
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158
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Byndloss MX, Litvak Y, Bäumler AJ. Microbiota-nourishing Immunity and Its Relevance for Ulcerative Colitis. Inflamm Bowel Dis 2019; 25:811-815. [PMID: 30698700 PMCID: PMC6769399 DOI: 10.1093/ibd/izz004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Indexed: 12/15/2022]
Abstract
An imbalance in our microbiota may contribute to many human diseases, but the mechanistic underpinnings of dysbiosis remain poorly understood. We argue that dysbiosis is secondary to a defect in microbiota-nourishing immunity, a part of our immune system that balances the microbiota to attain colonization resistance against environmental exposure to microorganisms. We discuss this new hypothesis and its implications for ulcerative colitis, an inflammatory bowel disease of the large intestine.
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Affiliation(s)
- Mariana X Byndloss
- Vanderbilt Institute for Infection, Immunology, and Inflammation and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA
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159
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Velazquez EM, Nguyen H, Heasley KT, Saechao CH, Gil LM, Rogers AWL, Miller BM, Rolston MR, Lopez CA, Litvak Y, Liou MJ, Faber F, Bronner DN, Tiffany CR, Byndloss MX, Byndloss AJ, Bäumler AJ. Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection. Nat Microbiol 2019; 4:1057-1064. [PMID: 30911125 PMCID: PMC6533147 DOI: 10.1038/s41564-019-0407-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 02/11/2019] [Indexed: 12/16/2022]
Abstract
Lack of reproducibility is a prominent problem in biomedical research. An important source of variation in animal experiments is the microbiome, but little is known about specific changes in the microbiota composition that cause phenotypic differences. Here we show that genetically similar laboratory mice obtained from four different commercial vendors exhibited marked phenotypic variation in their susceptibility to Salmonella infection. Fecal microbiota transplantation into germ-free mice replicated donor susceptibility, revealing that variability was due to changes in the gut microbiota composition. Co-housing of mice only partially transferred protection against Salmonella infection, suggesting that minority species within the gut microbiota might confer this trait. Consistent with this idea, we identified endogenous Enterobacteriaceae, a low abundance taxon, as keystone species responsible for variation in the susceptibility to Salmonella infection. Protection conferred by endogenous Enterobacteriaceae could be modeled by inoculating mice with probiotic Escherichia coli, which conferred resistance by using its aerobic metabolism to compete with Salmonella for resources. We conclude that a mechanistic understanding of phenotypic variation can accelerate development of strategies for enhancing the reproducibility of animal experiments.
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Affiliation(s)
- Eric M Velazquez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Henry Nguyen
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Keaton T Heasley
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Cheng H Saechao
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Lindsey M Gil
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andrew W L Rogers
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Brittany M Miller
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Matthew R Rolston
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Christopher A Lopez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Megan J Liou
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Franziska Faber
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Denise N Bronner
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Austin J Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, CA, USA.
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160
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Westreich ST, Ardeshir A, Alkan Z, Kable ME, Korf I, Lemay DG. Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization. MICROBIOME 2019; 7:41. [PMID: 30885266 PMCID: PMC6423747 DOI: 10.1186/s40168-019-0664-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/11/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. RESULTS Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes. CONCLUSIONS The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.
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Affiliation(s)
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, California USA
| | - Zeynep Alkan
- USDA ARS Western Human Nutrition Research Center, Davis, California USA
| | - Mary E. Kable
- USDA ARS Western Human Nutrition Research Center, Davis, California USA
- Department of Nutrition, University of California, Davis, California USA
| | - Ian Korf
- Genome Center, University of California, Davis, California USA
| | - Danielle G. Lemay
- Genome Center, University of California, Davis, California USA
- USDA ARS Western Human Nutrition Research Center, Davis, California USA
- Department of Nutrition, University of California, Davis, California USA
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161
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Yason JA, Liang YR, Png CW, Zhang Y, Tan KSW. Interactions between a pathogenic Blastocystis subtype and gut microbiota: in vitro and in vivo studies. MICROBIOME 2019; 7:30. [PMID: 30853028 PMCID: PMC6410515 DOI: 10.1186/s40168-019-0644-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/01/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Blastocystis is a common gut eukaryote detected in humans and animals. It has been associated with gastrointestinal disease in the past although recent metagenomic studies also suggest that it is a member of normal microbiota. This study investigates interactions between pathogenic human isolates belonging to Blastocystis subtype 7 (ST7) and bacterial representatives of the gut microbiota. RESULTS Generally, Blastocystis ST7 exerts a positive effect on the viability of representative gut bacteria except on Bifidobacterium longum. Gene expression analysis and flow cytometry indicate that the bacterium may be undergoing oxidative stress in the presence of Blastocystis. In vitro assays demonstrate that Blastocystis-induced host responses are able to decrease Bifidobacterium counts. Mice infected with Blastocystis also reveal a decrease in beneficial bacteria Bifidobacterium and Lactobacillus. CONCLUSIONS This study shows that particular isolates of Blastocystis ST7 cause changes in microbiota populations and potentially lead to an imbalance of the gut microbiota. This study suggests that certain isolates of Blastocystis exert their pathogenic effects through disruption of the gut microbiota and provides a counterpoint to the increasing reports indicating the commensal nature of this ubiquitous parasite.
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Affiliation(s)
- John Anthony Yason
- Laboratory of Molecular and Cellular Parasitology, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore
- Institute of Biology and Natural Sciences Research Institute, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Yi Ran Liang
- Laboratory of Molecular and Cellular Parasitology, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore
| | - Chin Wen Png
- Laboratory of Molecular and Cellular Parasitology, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore
| | - Yongliang Zhang
- Laboratory of Molecular and Cellular Parasitology, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore
| | - Kevin Shyong Wei Tan
- Laboratory of Molecular and Cellular Parasitology, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, 117545, Singapore.
- Microbiome Otago, Department of Microbiology and Immunology, University of Otago, PO Box 56 720, Cumberland St, Dunedin, 9054, Otago, New Zealand.
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162
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Underwood MA. Probiotics and the prevention of necrotizing enterocolitis. J Pediatr Surg 2019; 54:405-412. [PMID: 30241961 DOI: 10.1016/j.jpedsurg.2018.08.055] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Immaturity of the host immune system and alterations in the intestinal microbiome appear to be key factors in the pathogenesis of necrotizing enterocolitis (NEC). The aim of this paper is to weigh the evidence for the use of probiotics to prevent NEC in premature infants. METHODS Animal studies, randomized controlled trials, observational cohort studies and meta-analyses involving administration of probiotic products for the prevention of NEC were reviewed. This review of the evidence summarizes the available preclinical and clinical data. RESULTS In animal models probiotic microbes alter the intestinal microbiome, decrease inflammation and intestinal permeability and decrease the incidence and severity of experimental NEC. In randomized, placebo-controlled trials and cohort studies of premature infants, probiotic microbes decrease the risk of NEC, death and sepsis. CONCLUSION Evidence is strong for the prevention of NEC with the use of combination probiotics in premature infants who receive breast milk. The potential risks and benefits of probiotic administration to premature infants should be carefully reviewed with parents. TYPE OF STUDY Therapeutic. LEVEL OF EVIDENCE I.
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Affiliation(s)
- Mark A Underwood
- Division of Neonatology, University of California Davis, Ticon 2, Suite 253, 2516 Stockton Blvd, Sacramento, CA 95817, USA.
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163
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The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans. Nat Commun 2019; 10:905. [PMID: 30796211 PMCID: PMC6385246 DOI: 10.1038/s41467-019-08812-y] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/03/2019] [Indexed: 12/11/2022] Open
Abstract
β-Mannans are plant cell wall polysaccharides that are commonly found in human diets. However, a mechanistic understanding into the key populations that degrade this glycan is absent, especially for the dominant Firmicutes phylum. Here, we show that the prominent butyrate-producing Firmicute Roseburia intestinalis expresses two loci conferring metabolism of β-mannans. We combine multi-“omic” analyses and detailed biochemical studies to comprehensively characterize loci-encoded proteins that are involved in β-mannan capturing, importation, de-branching and degradation into monosaccharides. In mixed cultures, R. intestinalis shares the available β-mannan with Bacteroides ovatus, demonstrating that the apparatus allows coexistence in a competitive environment. In murine experiments, β-mannan selectively promotes beneficial gut bacteria, exemplified by increased R. intestinalis, and reduction of mucus-degraders. Our findings highlight that R. intestinalis is a primary degrader of this dietary fiber and that this metabolic capacity could be exploited to selectively promote key members of the healthy microbiota using β-mannan-based therapeutic interventions. How dietary β-mannans are utilized by gut Gram-positive bacteria is unclear. Here, the authors uncover the enzymatic pathway for β-mannan metabolism in Roseburia intestinalis and show that these polysaccharides promote beneficial gut bacteria, highlighting a potential for β-mannan-based therapeutic interventions.
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164
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Litvak Y, Bäumler AJ. The founder hypothesis: A basis for microbiota resistance, diversity in taxa carriage, and colonization resistance against pathogens. PLoS Pathog 2019; 15:e1007563. [PMID: 30789972 PMCID: PMC6383860 DOI: 10.1371/journal.ppat.1007563] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
| | - Andreas J. Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, United States of America
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165
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Vonaesch P, Anderson M, Sansonetti PJ. Pathogens, microbiome and the host: emergence of the ecological Koch's postulates. FEMS Microbiol Rev 2018; 42:273-292. [PMID: 29325027 DOI: 10.1093/femsre/fuy003] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Indexed: 02/07/2023] Open
Abstract
Even though tremendous progress has been made in the last decades to elucidate the mechanisms of intestinal homeostasis, dysbiosis and disease, we are only at the beginning of understanding the complexity of the gut ecosystem and the underlying interaction networks. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. Recent work in these domains clearly indicates that the 'traditional Koch's postulates', which state that a given pathogen leads to a distinct disease, are not valid for all 'infectious' diseases, but that a more complete and complex interpretation of Koch's postulates is needed in order to understand and explain them. This review summarises the current understanding of what defines a healthy gut ecosystem and highlights recent progress in uncovering the interplay between the host, its microbiota and invading intestinal pathogens. Based on these recent findings, we propose a new interpretation of Koch's postulates that we term 'ecological Koch's postulates'.
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Affiliation(s)
- Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
| | - Mark Anderson
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
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Abstract
An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.
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Affiliation(s)
- Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.
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Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans. mBio 2018; 9:mBio.02032-18. [PMID: 30401779 PMCID: PMC6222126 DOI: 10.1128/mbio.02032-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7–15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans. In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress. The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice “humanized” with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5’-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella. These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.
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169
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Tsaousis AD, Hamblin KA, Elliott CR, Young L, Rosell-Hidalgo A, Gourlay CW, Moore AL, van der Giezen M. The Human Gut Colonizer Blastocystis Respires Using Complex II and Alternative Oxidase to Buffer Transient Oxygen Fluctuations in the Gut. Front Cell Infect Microbiol 2018; 8:371. [PMID: 30406045 PMCID: PMC6204527 DOI: 10.3389/fcimb.2018.00371] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
Blastocystis is the most common eukaryotic microbe in the human gut. It is linked to irritable bowel syndrome (IBS), but its role in disease has been contested considering its widespread nature. This organism is well-adapted to its anoxic niche and lacks typical eukaryotic features, such as a cytochrome-driven mitochondrial electron transport. Although generally considered a strict or obligate anaerobe, its genome encodes an alternative oxidase. Alternative oxidases are energetically wasteful enzymes as they are non-protonmotive and energy is liberated in heat, but they are considered to be involved in oxidative stress protective mechanisms. Our results demonstrate that the Blastocystis cells themselves respire oxygen via this alternative oxidase thereby casting doubt on its strict anaerobic nature. Inhibition experiments using alternative oxidase and Complex II specific inhibitors clearly demonstrate their role in cellular respiration. We postulate that the alternative oxidase in Blastocystis is used to buffer transient oxygen fluctuations in the gut and that it likely is a common colonizer of the human gut and not causally involved in IBS. Additionally the alternative oxidase could act as a protective mechanism in a dysbiotic gut and thereby explain the absence of Blastocystis in established IBS environments.
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Affiliation(s)
- Anastasios D. Tsaousis
- RAPID Group, Laboratory of Molecular & Evolutionary Parasitology, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Karleigh A. Hamblin
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Catherine R. Elliott
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Luke Young
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Alicia Rosell-Hidalgo
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Campbell W. Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Anthony L. Moore
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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Ovesen S, Durack J, Kirk KF, Nielsen HL, Nielsen H, Lynch SV. Motility and biofilm formation of the emerging gastrointestinal pathogen Campylobacter concisus differs under microaerophilic and anaerobic environments. Gut Microbes 2018; 10:34-44. [PMID: 30252590 PMCID: PMC6363072 DOI: 10.1080/19490976.2018.1472201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Campylobacter concisus has been isolated from patients with gastroenteritis and inflammatory bowel disease (IBD), as well as healthy subjects. While strain differences may plausibly explain virulence differentials, an alternative hypothesis posits that the pathogenic potential of this species may depend on altered ecosystem conditions in the inflamed gut. One potential difference is oxygen availability, which is frequently increased under conditions of inflammation and is known to regulate bacterial virulence. Hence, we hypothesized that oxygen influences C. concisus physiology. We therefore characterized the effect of microaerophilic or anaerobic environments on C. concisus motility and biofilm formation, two important determinants of host colonization and dissemination. C. concisus isolates (n = 46) sourced from saliva, gut mucosal biopsies and feces of patients with IBD (n = 23), gastroenteritis (n = 8) and healthy subjects (n = 13), were used for this study. Capacity to form biofilms was determined using crystal violet assay, while assessment of dispersion through soft agar permitted motility to be assessed. No association existed between GI disease and either motility or biofilm forming capacity. Oral isolates exhibited significantly greater capacity for biofilm formation compared to fecal isolates (p<0.03), and showed a strong negative correlation between motility and biofilm formation (r = -0.7; p = 0.01). Motility significantly increased when strains were cultured under microaerophilic compared to anaerobic conditions (p<0.001). Increased biofilm formation under microaerophillic conditions was also observed for a subset of isolates. Hence, differences in oxygen availability appear to influence key physiological aspects of the opportunistic gastrointestinal pathogen C. concisus.
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Affiliation(s)
- Sandra Ovesen
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA,Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
| | - Juliana Durack
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Karina Frahm Kirk
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark
| | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Nielsen
- Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Susan V. Lynch
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA,CONTACT: Susan Lynch, ., Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA 94143, USA
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171
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Byndloss MX, Pernitzsch SR, Bäumler AJ. Healthy hosts rule within: ecological forces shaping the gut microbiota. Mucosal Immunol 2018; 11:1299-1305. [PMID: 29743614 DOI: 10.1038/s41385-018-0010-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/05/2018] [Indexed: 02/04/2023]
Abstract
A balanced gut microbiota is important for human health, but the mechanisms that maintain homeostasis are incompletely understood. Recent insights suggest the host plays a key role in shaping its gut microbiota to be beneficial. While host control in the small intestine curbs bacterial numbers to avoid competition for simple sugars and amino acids, the host limits oxygen availability in the large intestine to obtain microbial fermentation products from fiber. Epithelial cells are major players in imposing ecological control mechanisms, which involves the release of antimicrobial peptides by small-intestinal Paneth cells and maintenance of luminal anaerobiosis by epithelial hypoxia in the colon. Harnessing these epithelial control mechanisms for therapeutic means could provide a novel lynchpin for strategies to remediate dysbiosis.
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Affiliation(s)
- Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | | | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
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172
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The Intestinal Epithelium: Central Coordinator of Mucosal Immunity. Trends Immunol 2018; 39:677-696. [DOI: 10.1016/j.it.2018.04.002] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 12/15/2022]
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173
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Abstract
The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver diseases but also cancer and even neurodegenerative diseases. The human gut microbiota is viewed as a potential source of novel therapeutics. Between 2013 and 2017, the number of publications focusing on the gut microbiota was, remarkably, 12 900, which represents four-fifths of the total number of publications over the last 40 years that investigated this topic. This review discusses recent evidence of the impact of the gut microbiota on metabolic disorders and focus on selected key mechanisms. This review also aims to provide a critical analysis of the current knowledge in this field, identify putative key issues or problems and discuss misinterpretations. The abundance of metagenomic data generated on comparing diseased and healthy subjects can lead to the erroneous claim that a bacterium is causally linked with the protection or the onset of a disease. In fact, environmental factors such as dietary habits, drug treatments, intestinal motility and stool frequency and consistency are all factors that influence the composition of the microbiota and should be considered. The cases of the bacteria Prevotella copri and Akkermansia muciniphila will be discussed as key examples.
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Affiliation(s)
- Patrice D Cani
- Metabolism and Nutrition Research Group, Université catholique de Louvain, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, Brussels, Belgium
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174
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Casaburi G, Frese SA. Colonization of breastfed infants by Bifidobacterium longum subsp. infantis EVC001 reduces virulence gene abundance. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.humic.2018.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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175
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NADPH oxidases and ROS signaling in the gastrointestinal tract. Mucosal Immunol 2018; 11:1011-1023. [PMID: 29743611 DOI: 10.1038/s41385-018-0021-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 02/04/2023]
Abstract
Reactive oxygen species (ROS), initially categorized as toxic by-products of aerobic metabolism, have often been called a double-edged sword. ROS are considered indispensable when host defense and redox signaling is concerned and a threat in inflammatory or degenerative diseases. This generalization does not take in account the diversity of oxygen metabolites being generated, their physicochemical characteristics and their production by distinct enzymes in space and time. NOX/DUOX NADPH oxidases are the only enzymes solely dedicated to ROS production and the prime ROS producer for intracellular and intercellular communication due to their widespread expression and intricate regulation. Here we discuss new insights of how NADPH oxidases act via ROS as multifaceted regulators of the intestinal barrier in homeostasis, infectious disease and intestinal inflammation. A closer look at monogenic VEOIBD and commensals as ROS source supports the view of H2O2 as key beneficial messenger in the barrier ecosystem.
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176
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Associations between Gut Microbiota and Common Luminal Intestinal Parasites. Trends Parasitol 2018; 34:369-377. [DOI: 10.1016/j.pt.2018.02.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/09/2018] [Accepted: 02/13/2018] [Indexed: 02/08/2023]
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George AS, Cox CE, Desai P, Porwollik S, Chu W, de Moraes MH, McClelland M, Brandl MT, Teplitski M. Interactions of Salmonella enterica Serovar Typhimurium and Pectobacterium carotovorum within a Tomato Soft Rot. Appl Environ Microbiol 2018; 84:e01913-17. [PMID: 29247060 PMCID: PMC5812938 DOI: 10.1128/aem.01913-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Salmonella spp. are remarkably adaptable pathogens, and this adaptability allows these bacteria to thrive in a variety of environments and hosts. The mechanisms with which these pathogens establish within a niche amid the native microbiota remain poorly understood. Here, we aimed to uncover the mechanisms that enable Salmonella enterica serovar Typhimurium strain ATCC 14028 to benefit from the degradation of plant tissue by a soft rot plant pathogen, Pectobacterium carotovorum The hypothesis that in the soft rot, the liberation of starch (not utilized by P. carotovorum) makes this polymer available to Salmonella spp., thus allowing it to colonize soft rots, was tested first and proven null. To identify the functions involved in Salmonella soft rot colonization, we carried out transposon insertion sequencing coupled with the phenotypic characterization of the mutants. The data indicate that Salmonella spp. experience a metabolic shift in response to the changes in the environment brought on by Pectobacterium spp. and likely coordinated by the csrBC small regulatory RNA. While csrBC and flhD appear to be of importance in the soft rot, the global two-component system encoded by barA sirA (which controls csrBC and flhDC under laboratory conditions) does not appear to be necessary for the observed phenotype. Motility and the synthesis of nucleotides and amino acids play critical roles in the growth of Salmonella spp. in the soft rot.IMPORTANCE Outbreaks of produce-associated illness continue to be a food safety concern. Earlier studies demonstrated that the presence of phytopathogens on produce was a significant risk factor associated with increased Salmonella carriage on fruits and vegetables. Here, we genetically characterize some of the requirements for interactions between Salmonella and phytobacteria that allow Salmonella spp. to establish a niche within an alternate host (tomato). Pathways necessary for nucleotide synthesis, amino acid synthesis, and motility are identified as contributors to the persistence of Salmonella spp. in soft rots.
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Affiliation(s)
- Andrée S George
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
| | - Clayton E Cox
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
| | - Prerak Desai
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Weiping Chu
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Marcos H de Moraes
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Maria T Brandl
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Max Teplitski
- Soil and Water Science Department, Genetics Institute, University of Florida-IFAS, Gainesville, Florida, USA
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Abstract
In this review, we summarize existing knowledge regarding the effects of probiotics on necrotizing enterocolitis (NEC). We review the role of the microbiome in NEC and pre-clinical data on mechanisms of probiotic action. Next, we summarize existing randomized controlled trials and observational studies of probiotics to prevent NEC. We also summarize findings from several recent meta-analyses and report a new cumulative meta-analysis of probiotic trials. Finally, we review data from cohorts routinely using commercially available probiotics. Our goal is to inform clinicians about the risks and benefits of probiotics, which may be helpful for those considering use in preterm infants to prevent NEC, death, or sepsis.
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Affiliation(s)
- Ravi Mangal Patel
- Department of Pediatrics, Division of Neonatology, Emory University School of Medicine and Children's Healthcare of Atlanta, 2015 Uppergate Dr. NE, 3rd Floor, Atlanta, Georgia 30322.
| | - Mark A. Underwood
- Professor, Department of Pediatrics, Division of Neonatology, University of California Davis School of Medicine, Sacramento, CA
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179
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Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis. Proc Natl Acad Sci U S A 2018; 115:1605-1610. [PMID: 29378945 DOI: 10.1073/pnas.1714373115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The mature human gut microbiota is established during the first years of life, and altered intestinal microbiomes have been associated with several human health disorders. Escherichia coli usually represents less than 1% of the human intestinal microbiome, whereas in cystic fibrosis (CF), greater than 50% relative abundance is common and correlates with intestinal inflammation and fecal fat malabsorption. Despite the proliferation of E. coli and other Proteobacteria in conditions involving chronic gastrointestinal tract inflammation, little is known about adaptation of specific characteristics associated with microbiota clonal expansion. We show that E. coli isolated from fecal samples of young children with CF has adapted to growth on glycerol, a major component of fecal fat. E. coli isolates from different CF patients demonstrate an increased growth rate in the presence of glycerol compared with E. coli from healthy controls, and unrelated CF E. coli strains have independently acquired this growth trait. Furthermore, CF and control E. coli isolates have differential gene expression when grown in minimal media with glycerol as the sole carbon source. While CF isolates display a growth-promoting transcriptional profile, control isolates engage stress and stationary-phase programs, which likely results in slower growth rates. Our results indicate that there is selection of unique characteristics within the microbiome of individuals with CF, which could contribute to individual disease outcomes.
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180
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Abstract
Gut dysbiosis is associated with many non-communicable human diseases, but the mechanisms maintaining homeostasis remain incompletely understood. Recent insights suggest that during homeostasis, epithelial hypoxia limits oxygen availability in the colon, thereby maintaining a balanced microbiota that functions as a microbial organ, producing metabolites contributing to host nutrition, immune education and niche protection. Dysbiosis is characterized by a shift in the microbial community structure from obligate to facultative anaerobes, suggesting oxygen as an important ecological driver of microbial organ dysfunction. The ensuing disruption of gut homeostasis can lead to non- communicable disease because microbiota-derived metabolites are either depleted or generated at harmful concentrations. This Opinion article describes the concept that host control over the microbial ecosystem in the colon is critical for the composition and function of our microbial organ, which provides a theoretical framework for linking microorganisms to non-communicable diseases.
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Affiliation(s)
- Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, California 95616, USA
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181
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Proteobacteria: A Common Factor in Human Diseases. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9351507. [PMID: 29230419 PMCID: PMC5688358 DOI: 10.1155/2017/9351507] [Citation(s) in RCA: 634] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Microbiota represents the entire microbial community present in the gut host. It serves several functions establishing a mutualistic relation with the host. Latest years have seen a burst in the number of studies focusing on this topic, in particular on intestinal diseases. In this scenario, Proteobacteria are one of the most abundant phyla, comprising several known human pathogens. This review highlights the latest findings on the role of Proteobacteria not only in intestinal but also in extraintestinal diseases. Indeed, an increasing amount of data identifies Proteobacteria as a possible microbial signature of disease. Several studies demonstrate an increased abundance of members belonging to this phylum in such conditions. Major evidences currently involve metabolic disorders and inflammatory bowel disease. However, more recent studies suggest a role also in lung diseases, such as asthma and chronic obstructive pulmonary disease, but evidences are still scant. Notably, all these conditions are sustained by various degree of inflammation, which thus represents a core aspect of Proteobacteria-related diseases.
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183
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184
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Clark A, Mach N. The Crosstalk between the Gut Microbiota and Mitochondria during Exercise. Front Physiol 2017; 8:319. [PMID: 28579962 PMCID: PMC5437217 DOI: 10.3389/fphys.2017.00319] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/03/2017] [Indexed: 12/16/2022] Open
Abstract
Many physiological changes occur in response to endurance exercise in order to adapt to the increasing energy needs, mitochondria biogenesis, increased reactive oxygen species (ROS) production and acute inflammatory responses. Mitochondria are organelles within each cell that are crucial for ATP production and are also a major producer of ROS and reactive nitrogen species during intense exercise. Recent evidence shows there is a bidirectional interaction between mitochondria and microbiota. The gut microbiota have been shown to regulate key transcriptional co-activators, transcription factors and enzymes involved in mitochondrial biogenesis such as PGC-1α, SIRT1, and AMPK genes. Furthermore, the gut microbiota and its metabolites, such as short chain fatty acids and secondary bile acids, also contribute to host energy production, ROS modulation and inflammation in the gut by attenuating TNFα- mediated immune responses and inflammasomes such as NLRP3. On the other hand, mitochondria, particularly mitochondrial ROS production, have a crucial role in regulating the gut microbiota via modulating intestinal barrier function and mucosal immune responses. Recently, it has also been shown that genetic variants within the mitochondrial genome, could affect mitochondrial function and therefore the intestinal microbiota composition and activity. Diet is also known to dramatically modulate the composition of the gut microbiota. Therefore, studies targeting the gut microbiota can be useful for managing mitochondrial related ROS production, pro-inflammatory signals and metabolic limits in endurance athletes.
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Affiliation(s)
- Allison Clark
- Health Science Department, Open University of CataloniaBarcelona, Spain
| | - Núria Mach
- Health Science Department, Open University of CataloniaBarcelona, Spain.,UMR 1313, INRA, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
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185
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Mendes-Soares H, Chia N. Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology. Free Radic Biol Med 2017; 105:102-109. [PMID: 27989793 PMCID: PMC5401773 DOI: 10.1016/j.freeradbiomed.2016.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/27/2016] [Accepted: 12/12/2016] [Indexed: 12/27/2022]
Abstract
Interest in the human microbiome is at an all time high. The number of human microbiome studies is growing exponentially, as are reported associations between microbial communities and disease. However, we have not been able to translate the ever-growing amount of microbiome sequence data into better health. To do this, we need a practical means of transforming a disease-associated microbiome into a health-associated microbiome. This will require a framework that can be used to generate predictions about community dynamics within the microbiome under different conditions, predictions that can be tested and validated. In this review, using the gut microbiome to illustrate, we describe two classes of model that are currently being used to generate predictions about microbial community dynamics: ecological models and metabolic models. We outline the strengths and weaknesses of each approach and discuss the insights into the gut microbiome that have emerged from modeling thus far. We then argue that the two approaches can be combined to yield a community metabolic model, which will supply the framework needed to move from high-throughput omics data to testable predictions about how prebiotic, probiotic, and nutritional interventions affect the microbiome. We are confident that with a suitable model, researchers and clinicians will be able to harness the stream of sequence data and begin designing strategies to make targeted alterations to the microbiome and improve health.
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Affiliation(s)
- Helena Mendes-Soares
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA; Department of Bioengineering and Physiology, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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