{"id":1118607,"date":"2023-10-16T06:42:15","date_gmt":"2023-10-16T10:42:15","guid":{"rendered":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/uncategorized\/native-microbiome-dominates-over-host-factors-in-shaping-the-nature-com\/"},"modified":"2023-10-16T06:42:15","modified_gmt":"2023-10-16T10:42:15","slug":"native-microbiome-dominates-over-host-factors-in-shaping-the-nature-com","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/human-genetics\/native-microbiome-dominates-over-host-factors-in-shaping-the-nature-com\/","title":{"rendered":"Native microbiome dominates over host factors in shaping the &#8230; &#8211; Nature.com"},"content":{"rendered":"<p><p>        Xiao, Y., Zhai, Q., Zhang, H., Chen, W. & Hill, C. Gut        colonization mechanisms of Lactobacillus and        Bifidobacterium: an argument for personalized        designs. Annu. Rev. Food Sci. Technol. 12,        213233 (2021).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Walter, J., Maldonado-Gomez, M. X. & Martinez, I. To        engraft or not to engraft: an ecological framework for gut        microbiome modulation with live microbes. Curr. Opin.        Biotechnol. 49, 129139 (2018).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Mallon, C. A., Elsas, J. D. V. & Salles, J. F. Microbial        invasions: the process, patterns, and mechanisms. Trends        Microbiol. 23, 719729 (2015).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Porter, N. T. & Martens, E. C. Love thy neighbor: sharing        and cooperativity in the gut microbiota. Cell Host        Microbe 19, 745746 (2016).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Russell, B. J. et al. Intestinal transgene delivery with        native E. coli chassis allows persistent        physiological changes. Cell 185, 32633277        (2022).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Wang, J. et al. Genome adaptive evolution of        Lactobacillus casei under long-term antibiotic        selection pressures. BMC Genomics 18, 320        (2017).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Huang, S. et al. Candidate probiotic Lactiplantibacillus        plantarum HNU082 rapidly and convergently evolves within        human, mice, and zebrafish gut but differentially        influences the resident microbiome. Microbiome        9, 151 (2021).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Anal, A. K. & Singh, H. Recent advances in        microencapsulation of probiotics for industrial        applications and targeted delivery. Trends Food Sci.        Technol. 18, 240251 (2007).      <\/p>\n<p>        Article        CAS         Google Scholar      <\/p>\n<p>        Gao, P. et al. Screening and identification of probiotic        bifidobacterium from Mongolian children. Acta Microbiol.        Sin. 49, 210216 (2009).      <\/p>\n<p>        CAS         Google Scholar      <\/p>\n<p>        Sun, Z. et al. Complete genome sequence of probiotic        Bifidobacterium animalis subsp. lactis strain        V9. J. Bacteriol. 192, 40804081 (2010).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Yan, Y. et al. Probiotic Bifidobacterium lactis V9        attenuates hepatic steatosis and inflammation in rats with        non-alcoholic fatty liver disease. AMB Express        10, 101 (2020).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Diaz, R., Torres-Miranda, A., Orellana, G. & Garrido, D.        Comparative genomic analysis of novel Bifidobacterium        longum subsp. longum strains reveals functional divergence        in the human gut microbiota. Microorganisms        9, 1906 (2021).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Tenaillon, O. et al. Tempo and mode of genome evolution in        a 50,000-generation experiment. Nature 536,        165170 (2016).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Lieberman, T. D. et al. Genetic variation of a bacterial        pathogen within individuals with cystic fibrosis provides a        record of selective pressures. Nat. Genet.        46, 8287 (2014).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Good, B. H., McDonald, M. J., Barrick, J. E., Lenski, R. E.        & Desai, M. M. The dynamics of molecular evolution over        60,000 generations. Nature 551, 4550 (2017).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Kumar, R. et al. Evolutionary features in the structure and        function of bacterial toxins. Toxins 11, 15        (2019).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Whitlock, M. C. Fixation probability and time in subdivided        populations. Genetics 164, 767779 (2003).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Ford, C. B. et al. Use of whole genome sequencing to        estimate the mutation rate of Mycobacterium        tuberculosis during latent infection. Nat.        Genet. 43, 482486 (2011).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Eldholm, V. et al. Evolution of extensively drug-resistant        Mycobacterium tuberculosisfrom a susceptible        ancestor in a single patient. Genome Biol.        15, 490 (2014).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Walker, T. M. et al. Whole-genome sequencing to delineate        Mycobacterium tuberculosis outbreaks: a        retrospective observational study. Lancet Infect.        Dis. 13, 137146 (2013).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Eyre, D. W. et al. Diverse sources of C. difficile        infection identified on whole-genome sequencing. N.        Engl. J. Med. 369, 11951205 (2013).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        He, M. et al. Emergence and global spread of epidemic        healthcare-associated Clostridium difficile. Nat.        Genet. 45, 109113 (2013).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Young, B. C. et al. Evolutionary dynamics of Staphylococcus        aureus during progression from carriage to disease.        Proc. Natl Acad. Sci. USA 109, 45504555        (2012).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Didelot, X., Walker, A. S., Peto, T. E., Crook, D. W. &        Wilson, D. J. Within-host evolution of bacterial pathogens.        Nat. Rev. Microbiol. 14, 150162 (2016).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Wang, J. et al. Bacillus amyloliquefaciens FH-1        significantly affects cucumber seedlings and the        rhizosphere bacterial community but not soil. Sci.        Rep. 11, 12055 (2021).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Hofgaard, I. S. et al. Inoculum potential of        Fusarium spp. relates to tillage and straw        management in Norwegian fields of spring oats. Front.        Microbiol. 7, 556 (2016).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S.        Evolutionary dynamics of bacteria in the gut microbiome        within and across hosts. PLOS Biol. 17,        e3000102 (2019).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Caugant, D. A. & Brynildsrud, O. B. Neisseria meningitidis:        using genomics to understand diversity, evolution and        pathogenesis. Nat. Rev. Microbiol. 18, 8496        (2020).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Montecucco, C. & Rappuoli, R. Living dangerously: how        Helicobacter pylori survives in the human stomach.        Nat. Rev. Mol. Cell Biol. 2, 457466 (2001).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Ely, B. Recombination and gene loss occur simultaneously        during bacterial horizontal gene transfer. PLoS ONE        15, e0227987 (2020).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Newton, A. & Allebach, E. Gene transfer in Caulobacter        crescentus: polarized inheritance of genetic markers.        Genetics 80, 111 (1975).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Kilkenny, C., Browne, W. J., Cuthill, I. C., Emerson, M. &        Altman, D. G. Improving bioscience research reporting: the        ARRIVE guidelines for reporting animal research. PLoS        Biol. 8, e1000412 (2010).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Olm, M. R. et al. inStrain profiles population        microdiversity from metagenomic data and sensitively        detects shared microbial strains. Nat. Biotechnol.        39, 727736 (2021).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Hyatt, D. et al. Prodigal: prokaryotic gene recognition and        translation initiation site identification. BMC        Bioinform. 11, 119 (2010).      <\/p>\n<p>        Article         Google Scholar      <\/p>\n<p>        Desjardins, P. & Conklin, D. NanoDrop microvolume        quantitation of nucleic acids. J. Vis. Exp.        25, 2565 (2010).      <\/p>\n<p>                Google Scholar      <\/p>\n<p>        Lozano-Peral, D. et al. DNA degradation in human teeth        exposed to thermal stress. Sci. Rep. 11,        12118 (2021).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Beghini, F. et al. Integrating taxonomic, functional, and        strain-level profiling of diverse microbial communities        with bioBakery 3. Elife 10, e6508 (2021).      <\/p>\n<p><!-- Auto Generated --><\/p>\n<p>Read the rest here:<br \/>\n<a target=\"_blank\" href=\"https:\/\/www.nature.com\/articles\/s41522-023-00447-8\" title=\"Native microbiome dominates over host factors in shaping the ... - Nature.com\" rel=\"noopener\">Native microbiome dominates over host factors in shaping the ... - Nature.com<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p> Xiao, Y., Zhai, Q., Zhang, H., Chen, W. &#038; Hill, C. Gut colonization mechanisms of Lactobacillus and Bifidobacterium: an argument for personalized designs.  <a href=\"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/human-genetics\/native-microbiome-dominates-over-host-factors-in-shaping-the-nature-com\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[27],"tags":[],"class_list":["post-1118607","post","type-post","status-publish","format-standard","hentry","category-human-genetics"],"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1118607"}],"collection":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/comments?post=1118607"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1118607\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/media?parent=1118607"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/categories?post=1118607"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/tags?post=1118607"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}