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      The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice

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          Abstract

          This experiment was conducted to investigate the effect of exposure to high altitude and low oxygen on intestinal microbial communities using mice as an animal model. Fecal microbiota from mice housed in a control environment representing 2,200 meters (NC group) above sea level with 16% Oxygen and mice that were placed in a hypobaric chamber representing 5000 meters (HC group) above sea level with 11% Oxygen for 30 days, were analyzed by the HiSeq Illumina sequencing platform. The results showed a significant difference in beta diversity observed between the two groups, while no significant difference was observed in alpha diversity. Compared with the NC group, the relative abundance of class Epsilonproteobacteria, phlym Actinobacteria, class Erysipelotrichia and genus Helicobacter were significantly lower ( P<0.05), while the relative abundance of genus Alistipes was increased in the HC group; Phenotypic analysis showed no significant difference in aerobic, anaerobic, facultatively anaerobic, potentially pathogenic, stress tolerant, mobile element, biofilms formation, gram negative and gram positive between HC group and NC group; Functional analysis results showed significant differences in 34 gene functional metabolic pathways (carbohydrate digestion and absorption, energy metabolism, arachidonic acid metabolism, flavonoid biosynthesis, RIG-I-like receptor signaling pathway, etc) between HC group and NC group. Together, these findings suggest that exposure to high altitude and low oxygen had the potential to change the intestinal microbial communities, which potentially may modulate metabolic processes in mice.

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          T. Magoc, S. L. Salzberg (2013)
          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Intestinal microbiota, diet and health.

            Susan Power, Paul O'Toole, Catherine Stanton … (2014)
            The human intestine is colonised by 10¹³ to 10¹⁴ micro-organisms, the vast majority of which belong to the phyla Firmicutes and Bacteroidetes. Although highly stable over time, the composition and activities of the microbiota may be influenced by a number of factors including age, diet and antibiotic treatment. Although perturbations in the composition or functions of the microbiota are linked to inflammatory and metabolic disorders (e.g. inflammatory bowel diseases, irritable bowel syndrome and obesity), it is unclear at this point whether these changes are a symptom of the disease or a contributing factor. A better knowledge of the mechanisms through which changes in microbiota composition (dysbiosis) promote disease states is needed to improve our understanding of the causal relationship between the gut microbiota and disease. While evidence of the preventive and therapeutic effects of probiotic strains on diarrhoeal illness and other intestinal conditions is promising, the exact mechanisms of the beneficial effects are not fully understood. Recent studies have raised the question of whether non-viable probiotic strains can confer health benefits on the host by influencing the immune system. As the potential health effect of these non-viable bacteria depends on whether the mechanism of this effect is dependent on viability, future research needs to consider each probiotic strain on a case-by-case basis. The present review provides a comprehensive, updated overview of the human gut microbiota, the factors influencing its composition and the role of probiotics as a therapeutic modality in the treatment and prevention of diseases and/or restoration of human health.
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              Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States

              Audrie Lin, Elisabeth Bik, Elizabeth K. Costello … (2013)
              Background Our current understanding of the composition and stability of the human distal gut microbiota is based largely on studies of infants and adults living in developed countries. In contrast, little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries. Methodology/Principal Findings We compared the diversity, composition, and temporal stability of the fecal microbiota of healthy children, ages 9 to 14 years, living in an urban slum in Bangladesh with that of children of the same age range in an upper-middle class suburban community in the United States. We analyzed >8,000 near full-length 16S rRNA gene sequences and over 845,000 pyrosequencing reads of the 16S rRNA V1–V3 region. The distal gut of Bangladeshi children harbored significantly greater bacterial diversity than that of U.S. children, including novel lineages from several bacterial phyla. Bangladeshi and U.S. children had distinct fecal bacterial community membership and structure; the microbiota of Bangladeshi children was enriched in Prevotella, Butyrivibrio, and Oscillospira and depleted in Bacteroides relative to U.S. children (although similar to Bangladeshi adults). Furthermore, community membership and structure in Bangladeshi children was significantly less stable month-to-month than U.S. children. Conclusions/Significance Together, these results suggest that differing environmental or genetic factors may shape the microbiota of healthy children in the two countries. Further investigation is necessary to understand the mechanisms and factors that underlie these differences, and to incorporate these findings into new strategies for the prevention and treatment of childhood and adolescent diseases.
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                Author and article information

                Contributors
                Wei Zhang: Role: Funding acquisitionRole: Project administrationRole: Writing – review & editing
                Lefei Jiao: Role: Formal analysisRole: Writing – original draftRole: Writing – review & editing
                Ruixin Liu: Role: Investigation
                Yu Zhang: Role: Investigation
                Qiaorong Ji: Role: Investigation
                Huan Zhang: Role: Data curation
                Xiang Gao: Role: Investigation
                Yan Ma: Role: Data curation
                Hai Ning Shi:
                ORCID: http://orcid.org/0000-0002-5526-3233
                Role: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Bi-Song Yue: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 12 September 2018
                Publication date Collection: 2018
                Volume: 13
                Issue: 9
                Electronic Location Identifier: e0203701
                Affiliations
                [1 ] Research Center for High Altitude Medicine, Medical College of Qinghai University, Xining, Qinghai, China
                [2 ] Qinghai Key Laboratory of Science and Technology for High Altitude Medicine, Xining, China
                [3 ] Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
                [4 ] Weinan Central Hospital, Weinan, Shaanxi, China
                Sichuan University, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-5526-3233
                Article
                Publisher ID: PONE-D-18-12533
                DOI: 10.1371/journal.pone.0203701
                PMC ID: 6135514
                PubMed ID: 30208088
                SO-VID: 69fdad7a-0c89-4266-b025-ca5c65a4f793
                Copyright © © 2018 Zhang et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 25 April 2018
                Date accepted : 25 August 2018
                Page count
                Figures: 5, Tables: 2, Pages: 14
                Funding
                Funded by: National Natural Science Foundation of China (CN)
                Award ID: 31460240
                Award Recipient :
                ORCID: http://orcid.org/0000-0002-5526-3233
                Funded by: National Natural Science Foundation of China
                Award ID: 81560301
                Award Recipient :
                ORCID: http://orcid.org/0000-0002-5526-3233
                Funded by: National Natural Science Foundation of Qinghai
                Award ID: No. 2013-Z-905
                Award Recipient :
                ORCID: http://orcid.org/0000-0002-5526-3233
                This work was supported by the National Natural Science Foundation of China (No. 31460240, 81560301), and was also supported by the National Natural Science Foundation of Qinghai (No. 2013-Z-905). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Medical Microbiology
                Subject: Microbiome
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Genomics
                Subject: Microbial Genomics
                Subject: Microbiome
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Microbial Genomics
                Subject: Microbiome
                Subject: Biology and Life Sciences
                Subject: Cell Biology
                Subject: Hypoxia
                Subject: Biology and Life Sciences
                Subject: Anatomy
                Subject: Digestive System
                Subject: Gastrointestinal Tract
                Subject: Medicine and Health Sciences
                Subject: Anatomy
                Subject: Digestive System
                Subject: Gastrointestinal Tract
                Subject: Physical Sciences
                Subject: Chemistry
                Subject: Chemical Elements
                Subject: Oxygen
                Subject: Biology and Life Sciences
                Subject: Biochemistry
                Subject: Metabolism
                Subject: Metabolic Pathways
                Subject: Xenobiotic Metabolism
                Subject: Research and Analysis Methods
                Subject: Experimental Organism Systems
                Subject: Model Organisms
                Subject: Mouse Models
                Subject: Research and Analysis Methods
                Subject: Model Organisms
                Subject: Mouse Models
                Subject: Research and Analysis Methods
                Subject: Experimental Organism Systems
                Subject: Animal Models
                Subject: Mouse Models
                Subject: Biology and Life Sciences
                Subject: Biochemistry
                Subject: Metabolism
                Subject: Metabolic Pathways
                Subject: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Custom metadata
                Data Availability All relevant data are within the paper and its Supporting Information files.

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