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These studies mainly involved cultivation of gallstone-associated bacteria and 16S rRNA profiling, providing an indirect link between processes involved in gallstone formation by the bacteria\n                    <jats:italic>in-situ<\/jats:italic>\n                    . Here, we provide functional metagenomic evidence of a range of genes involved in bile stress response, biofilm formation, and anaerobic energy metabolism by Gram-negative\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    in pigmented gallstones from a 76-year-old male patient.\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    was also present in one cholesterol-type stone in a 30-year-old female patient who had additional cholesterol gallstones characterised by Gram-positive bacteria. Pigmented stones further revealed a predominance of genes involved in carbohydrate metabolism, whilst cholesterol stones indicated a profile dominanted by protein metabolism possibly reflecting known chemical differences between Gram-negative and Gram-positive biofilm matrices. Archaeal genes were not detected. Complementary carbon and hydrogen isotopic analyses of cholesterol within the patients\u2019 stones revealed homogeneity, suggesting a common diet or cholesterol biosynthesis pathway that has little influence on microbial composition. This pilot study provides a framework to study microbial processes that play a potential role in gallstone formation across markedly different types of stones and patient backgrounds.\n                  <\/jats:p>","DOI":"10.1038\/s41598-018-29571-8","type":"journal-article","created":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T06:41:57Z","timestamp":1531982517000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria"],"prefix":"10.1038","volume":"8","author":[{"given":"S. H.","family":"Kose","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K.","family":"Grice","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W. 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