Loss of function dysbiosis associated with antibiotics and high fat, high sugar diet.
Journal
The ISME journal
ISSN: 1751-7370
Titre abrégé: ISME J
Pays: England
ID NLM: 101301086
Informations de publication
Date de publication:
06 2019
06 2019
Historique:
received:
22
06
2018
accepted:
18
01
2019
revised:
17
01
2019
pubmed:
1
2
2019
medline:
23
11
2019
entrez:
1
2
2019
Statut:
ppublish
Résumé
The incidence of urinary stone disease (USD) has increased four-fold in 50 years. Oxalate, which is degraded exclusively by gut bacteria, is an important constituent in 80% of urinary stones. We quantified the effects of antibiotics and a high fat/high sugar (HFHS) diet on the microbial metabolism of oxalate in the gut. High and low oxalate-degrading mouse models were developed by administering fecal transplants from either the wild mammalian rodent Neotoma albigula or Swiss-Webster mice to Swiss-Webster mice, which produces a microbiota with or without the bacteria necessary for persistent oxalate metabolism, respectively. Antibiotics led to an acute loss of both transplant bacteria and associated oxalate metabolism. Transplant bacteria exhibited some recovery over time but oxalate metabolism did not. In contrast, a HFHS diet led to an acute loss of function coupled with a gradual loss of transplant bacteria, indicative of a shift in overall microbial metabolism. Thus, the effects of oral antibiotics on the microbiome form and function were greater than the effects of diet. Results indicate that both antibiotics and diet strongly influence microbial oxalate metabolism.
Identifiants
pubmed: 30700790
doi: 10.1038/s41396-019-0357-4
pii: 10.1038/s41396-019-0357-4
pmc: PMC6776053
doi:
Substances chimiques
Anti-Bacterial Agents
0
Oxalates
0
Sugars
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1379-1390Subventions
Organisme : NIDDK NIH HHS
ID : F32 DK102277
Pays : United States
Commentaires et corrections
Type : CommentIn
Références
Wilson I, Nicholson J. The role of gut microbiota in drug response. Curr Pharm Des. 2009;15:1519–23.
pubmed: 19442168
Maslowski KM, Mackay CR. Diet, gut microbiota and immune responses. Nat Immunol. 2010;12:5.
Sekirov I, Russell SL, Antunes LCM, Finlay BB. Gut microbiota in health and disease. Physiol Rev. 2010;90:859–904.
pubmed: 20664075
Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, et al. Host-gut microbiota metabolic interactions. Science. 2012;336:1262–7.
pubmed: 22674330
pmcid: 22674330
Kamada N, Seo S-U, Chen GY, Núñez G. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol. 2013;13:321.
pubmed: 23618829
Kohl KD, Weiss, Robert B, Cox J, Dale C, Dearing MD. Gut microbes of mammalian herbivores facillitate intake of plant toxins. Ecol Lett. 2014;17:1238–46.
pubmed: 25040855
pmcid: 25040855
Myers SP. The causes of intestinal dysbiosis: a review. Altern Med Rev. 2004;9:180–97.
pubmed: 15253677
Blaser MJ. Missing microbes: how the overuse of antibiotics is fueling our modern plagues. Macmillan; 2014; New York City, NY.
Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, Schmidt TM, et al. Decreased diversity of the fecal microbiome in recurrent Clostridium difficile—associated diarrhea. J Infect Dis. 2008;197:435–8.
pubmed: 18199029
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480.
pubmed: 19043404
pmcid: 19043404
Schippa S, Iebba V, Barbato M, Di Nardo G, Totino V, Checchi MP, et al. A distinctive ‘microbial signature’ in celiac pediatric patients. BMC Microbiol. 2010;10:175.
pubmed: 20565734
pmcid: 2906462
Durbán A, Abellán JJ, Jiménez-Hernández N, Ponce M, Ponce J, Sala T, et al. Assessing gut microbial diversity from feces and rectal mucosa. Microb Ecol. 2011;61:123–33.
pubmed: 20734040
Carroll IM, Ringel‐Kulka T, Siddle JP, Ringel Y. Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea‐predominant irritable bowel syndrome. Neurogastroenterol Motil. 2012;24:521.
pubmed: 22339879
pmcid: 3975596
Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, et al. Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst. 2013;105:1907–11.
pubmed: 24316595
pmcid: 3866154
Kang D-W, Park JG, Ilhan ZE, Wallstrom G, LaBaer J, Adams JB, et al. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS One. 2013;8:e68322.
pubmed: 23844187
pmcid: 3700858
Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, et al. Dietary intervention impact on gut microbial gene richness. Nature. 2013;500:585.
pubmed: 23985875
Abrahamsson T, Jakobsson H, Andersson AF, Björkstén B, Engstrand L, Jenmalm M. Low gut microbiota diversity in early infancy precedes asthma at school age. Clin Exp Allergy. 2014;44:842–50.
pubmed: 24330256
Sha S, Liang J, Chen M, Xu B, Liang C, Wei N, et al. Systematic review: faecal microbiota transplantation therapy for digestive and nondigestive disorders in adults and children. Aliment Pharmacol Ther. 2014;39:1003–32.
pubmed: 24641570
Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, et al. Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol. 2015;67:128–39.
pubmed: 25319745
pmcid: 4280348
Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–11.
pubmed: 16188921
pmcid: 1856500
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 2012;490:55–60.
Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008;6:e280.
pubmed: 19018661
pmcid: 2586385
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci. 2011;108:4554–61.
pubmed: 20847294
Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012;488:178.
pubmed: 22797518
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51.
pubmed: 2649005
pmcid: 2649005
Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science. 2011;332:970–4.
pubmed: 21596990
pmcid: 21596990
Brown K, Valenta K, Fisman D, Simor A, Daneman N. Hospital ward antibiotic prescribing and the risks of Clostridium difficile infection. JAMA Intern Med. 2015;175:626–33.
pubmed: 25705994
Candon S, Perez-Arroyo A, Marquet C, Valette F, Foray A-P, Pelletier B, et al. Antibiotics in early life alter the gut microbiome and increase disease incidence in a spontaneous mouse model of autoimmune insulin-dependent diabetes. PLoS One. 2015;10:e0125448.
pubmed: 25970503
pmcid: 4430542
Vangay P, Ward T, Gerber JS, Knights D. Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe. 2015;17:553–64.
pubmed: 25974298
pmcid: 5555213
Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet–induced obesity and diabetes in mice. Diabetes. 2008;57:1470–81.
pubmed: 18305141
Cani PD, Neyrinck AM, Fava F, Knauf C, Burcelin RG, Tuohy KM, et al. Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia. 2007;50:2374–83.
pubmed: 17823788
Everard A, Lazarevic V, Derrien M, Girard M, Muccioli GG, Neyrinck AM, et al. Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes. 2011;60:2775–86.
pubmed: 21933985
pmcid: 21933985
Neyrinck AM, Possemiers S, Druart C, Van de Wiele T, De Backer F, Cani PD, et al. Prebiotic effects of wheat arabinoxylan related to the increase in bifidobacteria, Roseburia and Bacteroides/Prevotella in diet-induced obese mice. PLoS One. 2011;6:e20944.
pubmed: 21695273
pmcid: 3111466
Neyrinck AM, Possemiers S, Verstraete W, De Backer F, Cani PD, Delzenne NM. Dietary modulation of clostridial cluster XIVa gut bacteria (Roseburia spp.) by chitin–glucan fiber improves host metabolic alterations induced by high-fat diet in mice. J Nutr Biochem. 2012;23:51–9.
pubmed: 21411304
Serino M, Luche E, Gres S, Baylac A, Bergé M, Cenac C, et al. Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota. Gut. 2012;61:543–53.
pubmed: 22110050
pmcid: 22110050
Lam YY, Ha CW, Campbell CR, Mitchell AJ, Dinudom A, Oscarsson J, et al. Increased gut permeability and microbiota change associate with mesenteric fat inflammation and metabolic dysfunction in diet-induced obese mice. PLoS One. 2012;7:e34233.
pubmed: 22457829
pmcid: 3311621
de La Serre CB, Ellis CL, Lee J, Hartman AL, Rutledge JC, Raybould HE. Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am J Physiol Gastrointest Liver Physiol. 2010;299:G440–8.
Wilck N, Olesen S, Matus M, Balogh A, Dechend R, Alm E, et al. A high-salt diet alters the composition of intestinal microbiota in mice. Hypertension. 2014;64:A321–A321.
Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J et al. Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut. 2015;64:1732–43.
pubmed: 25614621
pmcid: 5166700
Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, et al. Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nat Commun. 2015;6:7486.
pubmed: 26123276
pmcid: 4491183
Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun. 2012;80:62–73.
pubmed: 22006564
pmcid: 3255689
Frank DN, Amand ALS, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci. 2007;104:13780–5.
pubmed: 17699621
Gophna U, Sommerfeld K, Gophna S, Doolittle WF, van Zanten SJV. Differences between tissue-associated intestinal microfloras of patients with Crohn’s disease and ulcerative colitis. J Clin Microbiol. 2006;44:4136–41.
pubmed: 16988016
pmcid: 1698347
Ubeda C, Taur Y, Jenq RR, Equinda MJ, Son T, Samstein M, et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest. 2010;120:4332–41.
pubmed: 21099116
pmcid: 21099116
Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci. 2013;110:9066–71.
pubmed: 23671105
Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations. Nature. 2016;529:212.
pubmed: 26762459
pmcid: 26762459
Scales CD, Smith AC, Hanley JM, Saigal CS, Project UDiA. Prevalence of kidney stones in the United States. Eur Urol. 2012;62:160–5.
pubmed: 22498635
pmcid: 3362665
Reddy SC, Jacob JT, Varkey JB, Gaynes RP. Antibiotic use in US hospitals: quantification, quality measures and stewardship. Expert Rev Anti Infect Ther. 2015;13:843–54.
pubmed: 25925531
Van Boeckel TP, Gandra S, Ashok A, Caudron Q, Grenfell BT, Levin SA, et al. Global antibiotic consumption 2000 to 2010: an analysis of national pharmaceutical sales data. Lancet Infect Dis. 2014;14:742–50.
pubmed: 25022435
Aminov RI. A brief history of the antibiotic era: lessons learned and challenges for the future. Front Microbiol. 2010;1:134.
pubmed: 21687759
pmcid: 3109405
Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, et al. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nutr. 2005;81:341–54.
pubmed: 15699220
De SK, Liu X, Monga M. Changing trends in the American diet and the rising prevalence of kidney stones. Urology. 2014;84:1030–3.
pubmed: 25201150
Moe OW. Kidney stones: pathophysiology and medical management. lancet. 2006;367:333–44.
pubmed: 16443041
Holmes RP, Goodman HO, Assimos DG. Contribution of dietary oxalate to urinary oxalate excretion. Kidney Int. 2001;59:270–6.
pubmed: 11135080
Gasińska A, Gajewska D. Tea and coffee as the main sources of oxalate in diets of patients with kidney oxalate stones. Rocz Panstw Zakl Hig. 2007;58:61–67.
pubmed: 17711092
Noonan S, Savage G. Oxalate content of foods and its effect on humans. Asia Pac J Clin Nutr. 1999;8:64–74.
pubmed: 24393738
Conyers R, Bais R, Rofe A. The relation of clinical catastrophes, endogenous oxalate production, and urolithiasis. Clin Chem. 1990;36:1717–30.
pubmed: 2208646
Ribaya JD, Gershoff SN. Factors affecting endogenous oxalate synthesis and its excretion in feces and urine in rats. J Nutr. 1982;112:2161–9.
pubmed: 7131093
Knight J, Wood KD, Lange JN, Assimos DG, Holmes RP. Oxalate formation from glyoxal in erythrocytes. Urology. 2016;88:226. e211–5.
Lange JN, Wood KD, Knight J, Assimos DG, Holmes RP. Glyoxal formation and its role in endogenous oxalate synthesis. Adv Urol. 2012;2012:819202.
Holmes RP, Assimos DG. Glyoxylate synthesis, and its modulation and influence on oxalate synthesis. J Urol. 1998;160:1617–24.
pubmed: 9783918
Hodgkinson A. Oxalic acid in biology and medicine. Academic Press; London, New York; 1977.
Allison MJ, Dawson KA, Mayberry WR, Foss JG. Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract. Arch Microbiol. 1985;141:1–7.
pubmed: 3994481
Hatch M, Cornelius J, Allison M, Sidhu H, Peck A, Freel R. Oxalobacter sp. reduces urinary oxalate excretion by promoting enteric oxalate secretion. Kidney Int. 2006;69:691–8.
pubmed: 16518326
Hatch M, Gjymishka A, Salido EC, Allison MJ, Freel RW. Enteric oxalate elimination is induced and oxalate is normalized in a mouse model of primary hyperoxaluria following intestinal colonization with Oxalobacter. Am J Physiol-Gastrointest Liver Physiol. 2011;300:G461–9.
pubmed: 21163900
Miller AW, Kohl KD, Dearing MD. The gastrointestinal tract of the white-throated woodrat (Neotoma albigula) harbors distinct consortia of oxalate-degrading bacteria. Appl Environ Microbiol. 2014;80:1595–601.
pubmed: 24362432
pmcid: 3957601
Campieri C, Campieri M, Bertuzzi V, Swennen E, Matteuzzi D, Stefoni S, et al. Reduction of oxaluria after an oral course of lactic acid bacteria at high concentration. Kidney Int. 2001;60:1097–105.
pubmed: 11532105
Turroni S, Bendazzoli C, Dipalo SC, Candela M, Vitali B, Gotti R, et al. Oxalate-degrading activity in Bifidobacterium animalis subsp. lactis: impact of acidic conditions on the transcriptional levels of the oxalyl coenzyme A (CoA) decarboxylase and formyl-CoA transferase genes. Appl Environ Microbiol. 2010;76:5609–20.
pubmed: 20601517
pmcid: 2918965
Turroni S, Vitali B, Bendazzoli C, Candela M, Gotti R, Federici F, et al. Oxalate consumption by lactobacilli: evaluation of oxalyl‐CoA decarboxylase and formyl‐CoA transferase activity in Lactobacillus acidophilus. J Appl Microbiol. 2007;103:1600–9.
pubmed: 17953571
Baetz AL, Allison MJ. Purification and characterization of oxalyl-coenzyme A decarboxylase from Oxalobacter formigenes. J Bacteriol. 1989;171:2605–8.
pubmed: 2708315
pmcid: 209940
Baetz AL, Allison MJ. Purification and characterization of formyl-coenzyme A transferase from Oxalobacter formigenes. J Bacteriol. 1990;172:3537–40.
pubmed: 2361939
pmcid: 213325
Ruan Z-S, Anantharam V, Crawford IT, Ambudkar SV, Rhee SY, Allison MJ, et al. Identification, purification, and reconstitution of OxlT, the oxalate: formate antiport protein of Oxalobacter formigenes. J Biol Chem. 1992;267:10537–43.
pubmed: 1587834
Kaufman DW, Kelly JP, Curhan GC, Anderson TE, Dretler SP, Preminger GM, et al. Oxalobacter formigenes may reduce the risk of calcium oxalate kidney stones. J Am Soc Nephrol. 2008;19:1197–203.
pubmed: 18322162
pmcid: 2396938
Lange JN, Wood KD, Wong H, Otto R, Mufarrij PW, Knight J, et al. Sensitivity of human strains of Oxalobacter formigenes to commonly prescribed antibiotics. Urology. 2012;79:1286–9.
pubmed: 22656407
pmcid: 3569510
Miller AW, Dale C, Dearing MD. Microbiota diversification and crash induced by dietary oxalate in the mammalian herbivore Neotoma albigula. mSphere. 2017;2:e00428–17.
Miller AW, Oakeson KF, Dale C, Dearing MD. Effect of dietary oxalate on the gut microbiota of the mammalian herbivore Neotoma albigula. Appl Environ Microbiol. 2016;82:2669–75.
pubmed: 26896138
pmcid: 4836426
Miller AW, Dale C, Dearing MD. The induction of oxalate metabolism in vivo is more effective with functional microbial communities than with functional microbial species. mSystems. 2017;2:e00088–17.
pubmed: 28951890
pmcid: 5613171
Miller AW, Oakeson KF, Dale C, Dearing MD. Microbial community transplant results in increased and long-term oxalate degradation. Microbial Ecol. 2016;72:1–9.
pubmed: 27312892
pmcid: 5155304
Korat AVA, Willett WC, Hu FB. Diet, lifestyle, and genetic risk factors for type 2 diabetes: a review from the Nurses’ Health Study, Nurses’ Health Study 2, and Health Professionals’ Follow-up Study. Curr Nutr Rep. 2014;3:345–54.
Rankinen T, Sarzynski MA, Ghosh S, Bouchard C. Are there genetic paths common to obesity, cardiovascular disease outcomes, and cardiovascular risk factors? Circ Res. 2015;116:909–22.
pubmed: 25722444
pmcid: 4416656
Ng SC, Tang W, Leong RW, Chen M, Ko Y, Studd C et al. Environmental risk factors in inflammatory bowel disease: a population-based case-control study in Asia-Pacific. Gut. 2014;64:1063–71.
Zampini A, Nguyen A, Rose E, Monga M, Miller A. Reduced functional microbial network in patients with urolithiasis. Unpublished.
Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science. 2010;328:228–31.
pubmed: 20203013
pmcid: 4714868
Wolf JS, Bennett CJ, Dmochowski RR, Hollenbeck BK, Pearle MS, Schaeffer AJ. Best practice policy statement on urologic surgery antimicrobial prophylaxis. J Urol. 2008;179:1379–90.
pubmed: 18280509
Miller AW, Oakeson KF, Dale C, Dearing MD. The effect of dietary oxalate on the gut microbiota of the mammalian herbivore Neotoma albigula. Appl Environ Microbiol. 2016;AEM-00216.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.
pubmed: 22402401
pmcid: 22402401
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
pubmed: 20383131
pmcid: 20383131
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
pubmed: 20709691
pmcid: 20709691
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–200.
pubmed: 3150044
pmcid: 3150044
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1.
Lozupone C, Hamady M, Knight R. UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinforma. 2006;7:1.
Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8:e1002687.
pubmed: 3447976
pmcid: 3447976
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
pubmed: 14597658
pmcid: 14597658
Batagello CM, Manoj, Miller, AW. Urolithiasis: a case of missing microbes? J Endourol. 2018;32:995–1005.
Miller AW, Dearing D. The metabolic and ecological interactions of oxalate-degrading bacteria in the mammalian gut. Pathogens. 2013;2:636–52.
pubmed: 25437337
pmcid: 4235702
Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008;3:213–23.
pubmed: 18407065
pmcid: 3687783
Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124:837–48.
pubmed: 16497592
Shen W, Gaskins HR, McIntosh MK. Influence of dietary fat on intestinal microbes, inflammation, barrier function and metabolic outcomes. J Nutr Biochem. 2014;25:270–80.
pubmed: 24355793
Brinkworth GD, Noakes M, Clifton PM, Bird AR. Comparative effects of very low-carbohydrate, high-fat and high-carbohydrate, low-fat weight-loss diets on bowel habit and faecal short-chain fatty acids and bacterial populations. Br J Nutr. 2009;101:1493–502.
pubmed: 19224658
Miller AWC, David P, Kristina L, Lange, D. Identification of oxalate microbiome in non-stone forming individuals. Unpublished.
Ormerod KL, Wood DLA, Lachner N, Gellatly SL, Daly JN, Parsons JD, et al. Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome. 2016;4:1–17.
Rieu-Lesme F, Morvan B, Collins M, Fonty G, Willems A. A new H2/CO2-using acetogenic bacterium from the rumen: description of Ruminococcus schinkii sp. nov. FEMS Microbiol Lett. 1996;140:281–6.
pubmed: 8764491
Robeniol RZG, Serrano VD, Florendo PD, Aquino D, Cruz KJ, Divina CC. Acetogenic and acid utiliizng bacterial content analysis on ruminal fluid of water buffalo (Bubalus bubalis) calves. Int J Agric Technol. 2016;12:2065–71.
Bernalier A, Willems A, Leclerc M, Rochet V, Collins MD. Ruminococcus hydrogenotrophicus sp. nov., a new H2/CO2-utilizing acetogenic bacterium isolated from human feces. Arch Microbiol. 1996;166:176–83.
pubmed: 8703194
Duncan SH, Hold GL, Barcenilla A, Stewart CS, Flint HJ. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int J Syst Evol Microbiol. 2002;52:1615–20.
pubmed: 12361264