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      A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596

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          Abstract

          The infant intestinal microbiota is often colonized by two subspecies of Bifidobacterium longum: subsp. infantis ( B. infantis) and subsp. longum ( B. longum). Competitive growth of B. infantis in the neonate intestine has been linked to the utilization of human milk oligosaccharides (HMO). However, little is known how B. longum consumes HMO. In this study, infant-borne B. longum strains exhibited varying HMO growth phenotypes. While all strains efficiently utilized lacto- N-tetraose, certain strains additionally metabolized fucosylated HMO. B. longum SC596 grew vigorously on HMO, and glycoprofiling revealed a preference for consumption of fucosylated HMO. Transcriptomes of SC596 during early-stage growth on HMO were more similar to growth on fucosyllactose, transiting later to a pattern similar to growth on neutral HMO. B. longum SC596 contains a novel gene cluster devoted to the utilization of fucosylated HMO, including genes for import of fucosylated molecules, fucose metabolism and two α-fucosidases. This cluster showed a modular induction during early growth on HMO and fucosyllactose. This work clarifies the genomic and physiological variation of infant-borne B. longum to HMO consumption, which resembles B. infantis. The capability to preferentially consume fucosylated HMO suggests a competitive advantage for these unique B. longum strains in the breast-fed infant gut.

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          Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

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          The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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            CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

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              Human gut microbiome viewed across age and geography

              Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ between human populations when viewed from the perspective of component microbial lineages, encoded metabolic functions, stage of postnatal development, and environmental exposures, we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the representation of genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial species assemblages and functional gene repertoires were noted between individuals residing in the USA compared to the other two countries. These distinctive features are evident in early infancy as well as adulthood. In addition, the similarity of fecal microbiomes among family members extends across cultures. These findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations, and the impact of Westernization.
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                19 October 2016
                2016
                : 6
                : 35045
                Affiliations
                [1 ]Department of Viticulture & Enology, University of California , One Shields Ave. Davis, CA 95616, United States
                [2 ]Department of Foods for Health Institute and University of California , One Shields Ave. Davis, CA 95616, United States
                [3 ]Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile , Av. Vicuña Mackenna 4860, Santiago, Chile
                [4 ]Department of Chemistry, University of California , One Shields Ave. Davis, CA 95616, United States
                [5 ]Genome Center, University of California , One Shields Ave. Davis, CA 95616, United States
                [6 ]Centro de Genetica y Genomica, Facultad de Medicina, Clinica Alemana, Universidad del Desarrollo , Santiago, Chile
                [7 ]Department of Food Science & Technology, University of California , One Shields Ave. Davis, CA 95616, United States
                Author notes
                [*]

                Present address: University of Extremadura, Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Ctra. Avd. Adolfo Suarez s/n, 06007, Badajoz, Spain.

                Article
                srep35045
                10.1038/srep35045
                5069460
                27756904
                5a1babd5-0302-4785-a084-03a9347057bb
                Copyright © 2016, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 24 May 2016
                : 15 September 2016
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