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      Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

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          Abstract

          Recent reports have suggested the involvement of gut microbiota in the progression of colorectal cancer (CRC). We utilized pyrosequencing based analysis of 16S rRNA genes to determine the overall structure of microbiota in patients with colorectal cancer and healthy controls; we investigated microbiota of the intestinal lumen, the cancerous tissue and matched noncancerous normal tissue. Moreover, we investigated the mucosa-adherent microbial composition using rectal swab samples because the structure of the tissue-adherent bacterial community is potentially altered following bowel cleansing. Our findings indicated that the microbial structure of the intestinal lumen and cancerous tissue differed significantly. Phylotypes that enhance energy harvest from diets or perform metabolic exchange with the host were more abundant in the lumen. There were more abundant Firmicutes and less abundant Bacteroidetes and Proteobacteria in lumen. The overall microbial structures of cancerous tissue and noncancerous tissue were similar; howerer the tumor microbiota exhibited lower diversity. The structures of the intestinal lumen microbiota and mucosa-adherent microbiota were different in CRC patients compared to matched microbiota in healthy individuals. Lactobacillales was enriched in cancerous tissue, whereas Faecalibacterium was reduced. In the mucosa-adherent microbiota, Bifidobacterium, Faecalibacterium, and Blautia were reduced in CRC patients, whereas Fusobacterium, Porphyromonas, Peptostreptococcus, and Mogibacterium were enriched. In the lumen, predominant phylotypes related to metabolic disorders or metabolic exchange with the host, Erysipelotrichaceae, Prevotellaceae, and Coriobacteriaceae were increased in cancer patients. Coupled with previous reports, these results suggest that the intestinal microbiota is associated with CRC risk and that intestinal lumen microflora potentially influence CRC risk via cometabolism or metabolic exchange with the host. However, mucosa-associated microbiota potentially affects CRC risk primarily through direct interaction with the host.

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          Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex.

          We constructed error-correcting DNA barcodes that allow one run of a massively parallel pyrosequencer to process up to 1,544 samples simultaneously. Using these barcodes we processed bacterial 16S rRNA gene sequences representing microbial communities in 286 environmental samples, corrected 92% of sample assignment errors, and thus characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
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            The ecology and biotechnology of sulphate-reducing bacteria.

            Sulphate-reducing bacteria (SRB) are anaerobic microorganisms that use sulphate as a terminal electron acceptor in, for example, the degradation of organic compounds. They are ubiquitous in anoxic habitats, where they have an important role in both the sulphur and carbon cycles. SRB can cause a serious problem for industries, such as the offshore oil industry, because of the production of sulphide, which is highly reactive, corrosive and toxic. However, these organisms can also be beneficial by removing sulphate and heavy metals from waste streams. Although SRB have been studied for more than a century, it is only with the recent emergence of new molecular biological and genomic techniques that we have begun to obtain detailed information on their way of life.
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              Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice.

              The proportion of the human gut bacterial community that is recalcitrant to culture remains poorly defined. In this report, we combine high-throughput anaerobic culturing techniques with gnotobiotic animal husbandry and metagenomics to show that the human fecal microbiota consists largely of taxa and predicted functions that are represented in its readily cultured members. When transplanted into gnotobiotic mice, complete and cultured communities exhibit similar colonization dynamics, biogeographical distribution, and responses to dietary perturbations. Moreover, gnotobiotic mice can be used to shape these personalized culture collections to enrich for taxa suited to specific diets. We also demonstrate that thousands of isolates from a single donor can be clonally archived and taxonomically mapped in multiwell format to create personalized microbiota collections. Retrieving components of a microbiota that have coexisted in single donors who have physiologic or disease phenotypes of interest and reuniting them in various combinations in gnotobiotic mice should facilitate preclinical studies designed to determine the degree to which tractable bacterial taxa are able to transmit donor traits or influence host biology.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2012
                28 June 2012
                : 7
                : 6
                : e39743
                Affiliations
                [1 ]State Key Laboratory for Infectious Diseases Diagnostics and Treatment, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
                [2 ]Department of Anus and Intestine, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
                University of Bari & Consorzio Mario Negri Sud, Italy
                Author notes

                Conceived and designed the experiments: WC CX ZL FL. Performed the experiments: WC XT ZL FL. Analyzed the data: WC CX ZL FL. Contributed reagents/materials/analysis tools: WC FL ZL XT CX. Wrote the paper: WC ZL CX FL.

                Article
                PONE-D-12-01604
                10.1371/journal.pone.0039743
                3386193
                22761885
                1616feaa-ea3c-423b-92f1-e7fd6a4fce32
                Chen et al. 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
                : 12 January 2012
                : 25 May 2012
                Page count
                Pages: 9
                Categories
                Research Article
                Biology
                Ecology
                Microbial Ecology
                Microbiology
                Microbial Ecology
                Microbial Metabolism
                Medicine
                Gastroenterology and Hepatology
                Gastrointestinal Cancers
                Gastrointestinal Infections
                Oncology
                Cancer Risk Factors
                Environmental Causes of Cancer
                Nutritional Correlates of Cancer
                Cancers and Neoplasms
                Gastrointestinal Tumors
                Rectal Cancer
                Public Health
                Disease Ecology

                Uncategorized
                Uncategorized

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