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Research Paper

Dietary resistant starch supplementation increases gut luminal deoxycholic acid abundance in mice

Melanie A. Reutera Department of Surgery, Center for Alimentary and Metabolic Sciences, School of Medicine, University of California – Davis, Sacramento, CA, USA;b Department of Molecular Biosciences, School of Veterinary Medicine, University of California – Davis, Davis, CA, USAView further author information
,
Madelynn Tuckera Department of Surgery, Center for Alimentary and Metabolic Sciences, School of Medicine, University of California – Davis, Sacramento, CA, USA;b Department of Molecular Biosciences, School of Veterinary Medicine, University of California – Davis, Davis, CA, USAView further author information
,
Zara Marforia Department of Surgery, Center for Alimentary and Metabolic Sciences, School of Medicine, University of California – Davis, Sacramento, CA, USAView further author information
,
Rahaf Shishania Department of Surgery, Center for Alimentary and Metabolic Sciences, School of Medicine, University of California – Davis, Sacramento, CA, USA;b Department of Molecular Biosciences, School of Veterinary Medicine, University of California – Davis, Davis, CA, USAView further author information
,
Jessica Miranda Bustamantea Department of Surgery, Center for Alimentary and Metabolic Sciences, School of Medicine, University of California – Davis, Sacramento, CA, USA;b Department of Molecular Biosciences, School of Veterinary Medicine, University of California – Davis, Davis, CA, USAView further author information
,
Rosalinda Morenoa Department of Surgery, Center for Alimentary and Metabolic Sciences, School of Medicine, University of California – Davis, Sacramento, CA, USA;b Department of Molecular Biosciences, School of Veterinary Medicine, University of California – Davis, Davis, CA, USAView further author information
,
Michael L. Goodsonc Department of Environmental Toxicology, College of Agricultural and Environmental Sciences, University of California – Davis, Davis, CA, USAView further author information
,
Allison Ehrlichc Department of Environmental Toxicology, College of Agricultural and Environmental Sciences, University of California – Davis, Davis, CA, USAView further author information
,
Ameer Y. Tahad Department of Food Science and Technology, University of California - Davis, Davis, CA, USAView further author information
,
Pamela J. Leinb Department of Molecular Biosciences, School of Veterinary Medicine, University of California – Davis, Davis, CA, USAView further author information
,
Nikhil Joshie Bioinformatics Core, UC Davis Genome Center, University of California – Davis, Davis, CA, USAView further author information
,
Ilana Britof Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USAView further author information
,
Blythe Durbin-Johnsone Bioinformatics Core, UC Davis Genome Center, University of California – Davis, Davis, CA, USAView further author information
,
Renu Nandakumarg Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, NY, USAView further author information
&
Bethany P. Cummingsa Department of Surgery, Center for Alimentary and Metabolic Sciences, School of Medicine, University of California – Davis, Sacramento, CA, USA;b Department of Molecular Biosciences, School of Veterinary Medicine, University of California – Davis, Davis, CA, USACorrespondence[email protected]
View further author information
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Article: 2315632 | Received 23 Sep 2023, Accepted 02 Feb 2024, Published online: 20 Feb 2024

References

  • Thomas C, Gioiello A, Noriega L, Strehle A, Oury J, Rizzo G, Macchiarulo A, Yamamoto H, Mataki C, Pruzanski M. et al. TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab. 2009;10(3):167–18. doi:10.1016/j.cmet.2009.08.001.
  • Wang H, Chen J, Hollister K, Sowers LC, Forman BM. Endogenous bile acids are ligands for the nuclear receptor FXR/BAR. Mol Cell. 1999;3(5):543–553. doi:10.1016/S1097-2765(00)80348-2.
  • Di Ciaula A, Garruti G, Lunardi Baccetto R, Molina-Molina E, Bonfrate L, Wang DQ, Portincasa P. Bile acid physiology. Ann Hepatol. 2017;16 (Suppl 1):S4–S14. doi:10.5604/01.3001.0010.5493.
  • Chiang JY. Bile acid metabolism and signaling. Compr Physiol. 2013;3:1191–1212.
  • Charach G, Grosskopf I, Rabinovich A, Shochat M, Weintraub M, Rabinovich P. The association of bile acid excretion and atherosclerotic coronary artery disease. Therap Adv Gastroenterol. 2011;4(2):95–101. doi:10.1177/1756283X10388682.
  • MahmoudianDehkordi S, Arnold M, Nho K, Ahmad S, Jia W, Xie G, Louie G, Kueider‐Paisley A, Moseley MA, Thompson JW. et al. Altered bile acid profile associates with cognitive impairment in Alzheimer’s disease—an emerging role for gut microbiome. Alzheimer’s & Dementia. 2019;15(1):76–92. doi:10.1016/j.jalz.2018.07.217.
  • Mullish BH, McDonald JAK, Pechlivanis A, Allegretti JR, Kao D, Barker GF, Kapila D, Petrof EO, Joyce SA, Gahan CGM. et al. Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut. 2019;68(10):1791–1800. doi:10.1136/gutjnl-2018-317842.
  • Weingarden AR, Chen C, Bobr A, Yao D, Lu Y, Nelson VM, Sadowsky MJ, Khoruts A. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am J Physiol Gastrointest Liver Physiol. 2014;306(4):G310–9. doi:10.1152/ajpgi.00282.2013.
  • Danne C, Rolhion N, Sokol H. Recipient factors in faecal microbiota transplantation: one stool does not fit all. Nat Rev Gastroenterol Hepatol. 2021;18(7):503–513. doi:10.1038/s41575-021-00441-5.
  • Ridlon JM, Harris SC, Bhowmik S, Kang DJ, Hylemon PB. Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes. 2016;7(1):22–39. doi:10.1080/19490976.2015.1127483.
  • Mallonee DH, Hylemon PB. Sequencing and expression of a gene encoding a bile acid transporter from Eubacterium sp. strain VPI 12708. J Bacteriol. 1996;178(24):7053–7058. doi:10.1128/jb.178.24.7053-7058.1996.
  • Song Z, Cai Y, Lao X, Wang X, Lin X, Cui Y, Kalavagunta PK, Liao J, Jin L, Shang J. et al. Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome. Microbiome. 2019;7(1):9. doi:10.1186/s40168-019-0628-3.
  • Rath S, Rud T, Karch A, Pieper DH, Vital M. Pathogenic functions of host microbiota. Microbiome. 2018;6(1):174. doi:10.1186/s40168-018-0542-0.
  • Hirano S, Nakama R, Tamaki M, Masuda N, Oda H. Isolation and characterization of thirteen intestinal microorganisms capable of 7 alpha-dehydroxylating bile acids. Appl Environ Microbiol. 1981;41(3):737–745. doi:10.1128/aem.41.3.737-745.1981.
  • Lee JW, Cowley ES, Wolf PG, Doden HL, Murai T, Caicedo KYO, Ly LK, Sun F, Takei H, Nittono H. et al. Formation of secondary allo-bile acids by novel enzymes from gut firmicutes. Gut Microbes. 2022;14(1):2132903. doi:10.1080/19490976.2022.2132903.
  • Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S. et al. Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature. 2021;599(7885):458–464. doi:10.1038/s41586-021-03832-5.
  • Martinez I, Kim J, Duffy PR, Schlegel VL, Walter J, Heimesaat MM. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One. 2010;5(11):e15046. doi:10.1371/journal.pone.0015046.
  • Dobranowski PA, Stintzi A. Resistant starch, microbiome, and precision modulation. Gut Microbes. 2021;13(1):1926842. doi:10.1080/19490976.2021.1926842.
  • Bodinham CL, Smith L, Thomas EL, Bell JD, Swann JR, Costabile A, Russell-Jones D, Umpleby AM, Robertson MD. Efficacy of increased resistant starch consumption in human type 2 diabetes. Endocr Connect. 2014;3(2):75–84. doi:10.1530/EC-14-0036.
  • Lange K, Hugenholtz F, Jonathan MC, Schols HA, Kleerebezem M, Smidt H, Müller M, Hooiveld GJEJ. Comparison of the effects of five dietary fibers on mucosal transcriptional profiles, and luminal microbiota composition and SCFA concentrations in murine colon. Mol Nutr Food Res. 2015;59(8):1590–1602. doi:10.1002/mnfr.201400597.
  • Arifuzzaman M, Won TH, Li TT, Yano H, Digumarthi S, Heras AF, Zhang W, Parkhurst CN, Kashyap S, Jin W-B. et al. Inulin fibre promotes microbiota-derived bile acids and type 2 inflammation. Nature. 2022;611(7936):578–584. doi:10.1038/s41586-022-05380-y.
  • Makki K, Brolin H, Petersen N, Henricsson M, Christensen DP, Khan MT, Wahlström A, Bergh P-O, Tremaroli V, Schoonjans K. et al. 6α-hydroxylated bile acids mediate TGR5 signalling to improve glucose metabolism upon dietary fiber supplementation in mice. Gut. 2023;72(2):314–324. doi:10.1136/gutjnl-2021-326541.
  • Charrier JA, Martin RJ, McCutcheon KL, Raggio AM, Goldsmith F, Goita M, Senevirathne RN, Brown IL, Pelkman C, Zhou J. et al. High fat diet partially attenuates fermentation responses in rats fed resistant starch from high-Amylose Maize. Obesity. 2013;21(11):2350–2355. doi:10.1002/oby.20362.
  • Vidrine K, Ye J, Martin RJ, McCutcheon KL, Raggio AM, Pelkman C, Durham HA, Zhou J, Senevirathne RN, Williams C. et al. Resistant starch from high amylose maize (HAM-RS2) and dietary butyrate reduce abdominal fat by a different apparent mechanism. Obesity (Silver Spring). 2014;22(2):344–348. doi:10.1002/oby.20501.
  • van Munster IP, Tangerman A, Nagengast FM. Effect of resistant starch on colonic fermentation, bile acid metabolism, and mucosal proliferation. Dig Dis Sci. 1994;39(4):834–842. doi:10.1007/BF02087431.
  • Abadie C, Hug M, Kubli C, Gains N. Effect of cyclodextrins and undigested starch on the loss of chenodeoxycholate in the faeces. Biochem J. 1994;299(Pt 3):725–730. doi:10.1042/bj2990725.
  • Ebihara K, Shiraishi R, Okuma K. Hydroxypropyl-modified potato starch increases fecal bile acid excretion in rats. J Nutr. 1998;128(5):848–854. doi:10.1093/jn/128.5.848.
  • Lopez HW, Levrat-Verny MA, Coudray C, Besson C, Krespine V, Messager A, Demigné C, Rémésy C. Class 2 resistant starches lower plasma and liver lipids and improve mineral retention in rats. J Nutr. 2001;131(4):1283–1289. doi:10.1093/jn/131.4.1283.
  • Trautwein EA, Forgbert K, Rieckhoff D, Erbersdobler HF. Impact of β-cyclodextrin and resistant starch on bile acid metabolism and fecal steroid excretion in regard to their hypolipidemic action in hamsters1Presented in part at experimental biology 98, 18–22 April, 1998, San Francisco, CA, USA.1. Biochim Biophys Acta. 1999;1437(1):1–12. doi:10.1016/S0005-2760(98)00174-X.
  • Ridlon JM, Kang DJ, Hylemon PB. Bile salt biotransformations by human intestinal bacteria. J Lipid Res. 2006;47(2):241–259. doi:10.1194/jlr.R500013-JLR200.
  • Ridlon JM, Hylemon PB. Identification and characterization of two bile acid coenzyme a transferases from clostridium scindens, a bile acid 7α-dehydroxylating intestinal bacterium. J Lipid Res. 2012;53(1):66–76. doi:10.1194/jlr.M020313.
  • Kawamata Y, Fujii R, Hosoya M, Harada M, Yoshida H, Miwa M, Fukusumi S, Habata Y, Itoh T, Shintani Y. et al. A G protein-coupled receptor responsive to bile acids. J Biol Chem. 2003;278(11):9435–9440. doi:10.1074/jbc.M209706200.
  • Chiang JYL, Ferrell JM. Up to date on cholesterol 7 alpha-hydroxylase (CYP7A1) in bile acid synthesis. Liver Res. 2020;4(2):47–63. doi:10.1016/j.livres.2020.05.001.
  • Takahashi S, Fukami T, Masuo Y, Brocker CN, Xie C, Krausz KW, Wolf CR, Henderson CJ, Gonzalez FJ. Cyp2c70 is responsible for the species difference in bile acid metabolism between mice and humans. J Lipid Res. 2016;57(12):2130–2137. doi:10.1194/jlr.M071183.
  • Dawson PA, Lan T, Rao A. Bile acid transporters. J Lipid Res. 2009;50(12):2340–2357. doi:10.1194/jlr.R900012-JLR200.
  • Bendiks ZA, Guice J, Coulon D, Raggio AM, Page RC, Carvajal-Aldaz DG, Luo M, Welsh DA, Marx BD, Taylor CM. et al. Resistant starch type 2 and whole grain maize flours enrich different intestinal bacteria and metatranscriptomes. J Funct Foods. 2022;90:104982. doi:10.1016/j.jff.2022.104982.
  • Bendiks ZA, Knudsen KEB, Keenan MJ, Marco ML. Conserved and variable responses of the gut microbiome to resistant starch type 2. Nutr Res. 2020;77:12–28. doi:10.1016/j.nutres.2020.02.009.
  • Fujio-Vejar S, Vasquez Y, Morales P, Magne F, Vera-Wolf P, Ugalde JA, Navarrete P, Gotteland M. The gut microbiota of healthy Chilean subjects reveals a high abundance of the phylum verrucomicrobia. Front Microbiol. 2017;8:1221. doi:10.3389/fmicb.2017.01221.
  • Belzer C, de Vos WM. Microbes inside—from diversity to function: the case of Akkermansia. ISME J. 2012;6(8):1449–1458. doi:10.1038/ismej.2012.6.
  • Hidalgo-Cantabrana C, Delgado S, Ruiz L, Ruas-Madiedo P, Sanchez B, Margolles A, Britton RA, Cani PD. Bifidobacteria and their health-promoting effects. Microbiol Spectr. 2017;5(3):73–98. doi:10.1128/microbiolspec.BAD-0010-2016.
  • Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Curr Opin Gastroenterol. 2014;30(3):332–338. doi:10.1097/MOG.0000000000000057.
  • Ridlon JM, Kang DJ, Hylemon PB. Isolation and characterization of a bile acid inducible 7α-dehydroxylating operon in clostridium hylemonae TN271. Anaerobe. 2010;16(2):137–146. doi:10.1016/j.anaerobe.2009.05.004.
  • Vital M, Rud T, Rath S, Pieper DH, Schluter D. Diversity of bacteria exhibiting bile acid-inducible 7alpha-dehydroxylation genes in the human gut. Comput Struct Biotechnol J. 2019;17:1016–1019. doi:10.1016/j.csbj.2019.07.012.
  • Sybille T, June Z, Michael K, Roy M, Maria LM. The intestinal microbiota in aged mice is modulated by dietary resistant starch and correlated with improvements in host responses. FEMS Microbiol Ecol. 2013;83(2):299–309. doi:10.1111/j.1574-6941.2012.01475.x.
  • Lei S, He S, Li X, Zheng B, Zhang Y, Zeng H. Effect of lotus seed resistant starch on small intestinal flora and bile acids in hyperlipidemic rats. Food Chem. 2023;404:134599. doi:10.1016/j.foodchem.2022.134599.
  • Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature. 2015;517(7533):205–208. doi:10.1038/nature13828.
  • Funabashi M, Grove TL, Wang M, Varma Y, McFadden ME, Brown LC, Guo C, Higginbottom S, Almo SC, Fischbach MA. A metabolic pathway for bile acid dehydroxylation by the gut microbiome. Nature. 2020;582(7813):566–570. doi:10.1038/s41586-020-2396-4.
  • Larabi AB, Masson HLP, Baumler AJ. Bile acids as modulators of gut microbiota composition and function. Gut Microbes. 2023;15(1):2172671. doi:10.1080/19490976.2023.2172671.
  • Guzior DV, Quinn RA. Review: microbial transformations of human bile acids. Microbiome. 2021;9(1):140. doi:10.1186/s40168-021-01101-1.
  • Devendran S, Mendez-Garcia C, Ridlon JM. Identification and characterization of a 20β-HSDH from the anaerobic gut bacterium Butyricicoccus desmolans ATCC 43058. J Lipid Res. 2017;58(5):916–925. doi:10.1194/jlr.M074914.
  • Yang Y, Chi L, Liu CW, Hsiao YC, Lu K. Chronic Arsenic Exposure Perturbs Gut Microbiota and Bile Acid Homeostasis in Mice. Chem Res Toxicol. 2023;36(7):1037–1043. doi:10.1021/acs.chemrestox.2c00410.
  • Owen RW, Henly PJ, Thompson MH, Hill MJ. Steroids and cancer: faecal bile acid screening for early detection of cancer risk. J Steroid Biochem. 1986;24(1):391–394. doi:10.1016/0022-4731(86)90088-9.
  • Herp S, Durai Raj AC, Salvado Silva M, Woelfel S, Stecher B. The human symbiont mucispirillum schaedleri: causality in health and disease. Med Microbiol Immunol. 2021;210(4):173–179. doi:10.1007/s00430-021-00702-9.
  • Gruner E, Steigerwalt AG, Hollis DG, Weyant RS, Weaver RE, Moss CW, Daneshvar M, Brown JM, Brenner DJ. Human infections caused by Brevibacterium casei, formerly CDC groups B-1 and B-3. J Clin Microbiol. 1994;32(6):1511–1518. doi:10.1128/jcm.32.6.1511-1518.1994.
  • Tian J, Wang L, Liu P, Geng Y, Zhu G, Zheng R, Liu Z, Zhao Y, Yang J, Peng F. Deinococcus psychrotolerans sp. nov., isolated from soil on the South Shetland Islands, Antarctica. Int J Syst Evol Microbiol. 2019;69(12):3696–3701. doi:10.1099/ijsem.0.003484.
  • Sakamoto M, Huang Y, Umeda M, Ishikawa I, Benno Y. Prevotella multiformissp. nov., isolated from human subgingival plaque. Int J Syst Evol Microbiol. 2005;55(2):815–819. doi:10.1099/ijs.0.63451-0.
  • Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105–108. doi:10.1126/science.1208344.
  • Ekundayo TC, Igere BE, Iwu CD, Oluwafemi YD, Tiamiyu AM, Adesina IA, Anuoluwa IA, Ekundayo EA, Bello OO, Olaniyi OO. et al. Prevalence of laribacter hongkongensis in food and environmental matrices: a systematic review and meta-analysis. Food Microbiol. 2022;107:104089. doi:10.1016/j.fm.2022.104089.
  • Baek C, Shin SK, Yi H. Flavobacterium magnum sp. nov., Flavobacterium pallidum sp. nov., Flavobacterium crocinum sp. nov. and Flavobacterium album sp. nov. Int J Syst Evol Microbiol. 2018;68(12):3837–3843. doi:10.1099/ijsem.0.003067.
  • Siddiqi MZ, Sambath P, Im WT. Phnomibacter ginsenosidimutans gen. nov., sp. nov., a novel glycoside hydrolase positive bacterial strain with ginsenoside hydrolysing activity. Int J Syst Evol Microbiol. 2021;71(5):71. doi:10.1099/ijsem.0.004793.
  • Ng SC, Kamm MA, Yeoh YK, Chan PKS, Zuo T, Tang W, Sood A, Andoh A, Ohmiya N, Zhou Y. et al. Scientific frontiers in faecal microbiota transplantation: joint document of Asia-Pacific Association of Gastroenterology (APAGE) and Asia-Pacific Society for Digestive Endoscopy (APSDE). Gut. 2020;69(1):83–91. doi:10.1136/gutjnl-2019-319407.
  • Kootte RS, Levin E, Salojarvi J, Smits LP, Hartstra AV, Udayappan SD, Hermes G, Bouter KE, Koopen AM, Holst JJ. et al. Improvement of insulin sensitivity after lean donor feces in Metabolic Syndrome is Driven by baseline intestinal microbiota composition. Cell Metab. 2017;26(4):611–619.e6. doi:10.1016/j.cmet.2017.09.008.
  • Weingarden AR, Dosa PI, DeWinter E, Steer CJ, Shaughnessy MK, Johnson JR, Khoruts A, Sadowsky MJ. Changes in colonic bile acid composition following fecal microbiota transplantation are sufficient to control clostridium difficile germination and growth. PloS One. 2016;11(1):e0147210. doi:10.1371/journal.pone.0147210.
  • Allegretti JR, Kassam Z, Mullish BH, Chiang A, Carrellas M, Hurtado J, Marchesi JR, McDonald JAK, Pechlivanis A, Barker GF. et al. Effects of fecal microbiota transplantation with oral capsules in obese patients. Clin Gastroenterol Hepatol. 2020;18(4):855–863.e2. doi:10.1016/j.cgh.2019.07.006.
  • Allegretti JR, Kassam Z, Hurtado J, Marchesi JR, Mullish BH, Chiang A, Thompson CC, Cummings BP. Impact of fecal microbiota transplantation with capsules on the prevention of metabolic syndrome among patients with obesity. Hormones (Athens). 2021;20(1):209–211. doi:10.1007/s42000-020-00265-z.
  • Zeng H, Grapov D, Jackson MI, Fahrmann J, Fiehn O, Combs GF. Integrating multiple analytical datasets to compare metabolite profiles of mouse colonic-cecal contents and feces. Metabolites. 2015;5(3):489–501. doi:10.3390/metabo5030489.
  • Urso A, Leiva-Juarez MM, Briganti DF, Aramini B, Benvenuto L, Costa J, Nandakumar R, Gomez EA, Robbins HY, Shah L. et al. Aspiration of conjugated bile acids predicts adverse lung transplant outcomes and correlates with airway lipid and cytokine dysregulation. J Heart Lung Transplant. 2021;40(9):998–1008. doi:10.1016/j.healun.2021.05.007.
  • Holter MM, Phuong DJ, Lee I, Saikia M, Weikert L, Fountain S, Anderson ET, Fu Q, Zhang S, Sloop KW. et al. 14-3-3-zeta mediates GLP-1 receptor agonist action to alter α cell proglucagon processing. Sci Adv. 2022;8(29):eabn3773. doi:10.1126/sciadv.abn3773.
  • Bustamante JM, Dawson T, Loeffler C, Marfori Z, Marchesi JR, Mullish BH, Thompson CC, Crandall KA, Rahnavard A, Allegretti JR. et al. Impact of Fecal Microbiota Transplantation on Gut Bacterial Bile Acid Metabolism in Humans. Nutrients. 2022;14(24):14. doi:10.3390/nu14245200.
  • Petersen KR, Streett DA, Gerritsen AT, Hunter SS, Settles ML. Super deduper, fast PCR duplicate detection in fastq files. Association for Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics; 2015;491–492. Atlanta, GA.
  • Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–359. doi:10.1038/nmeth.1923.
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078–2079. doi:10.1093/bioinformatics/btp352.
  • Quinlan AR, Hall IM. Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–842. doi:10.1093/bioinformatics/btq033.
  • Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20(1):257. doi:10.1186/s13059-019-1891-0.
  • Dabdoub S. kraken-biom: Enabling interoperative format conversion for Kraken results (Version 1.2) [Software]. 2016.
  • McMurdie PJ, Holmes S, Watson M. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217. doi:10.1371/journal.pone.0061217.
  • Torgerson WS. Theory and methods of scaling. New York: Wiley; 1958.
  • Bray JR, Curtis JT. An ordination of the upland forest communities of Southern Wisconsin. Ecol Monogr. 1957;27(4):325–349. doi:10.2307/1942268.
  • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106. doi:10.1186/gb-2010-11-10-r106.
  • Mallick H, Chatterjee S, Chowdhury S, Chatterjee S, Rahnavard A, Hicks SC. Differential expression of single-cell RNA-seq data using Tweedie models. Stat Med. 2022;41(18):3492–3510. doi:10.1002/sim.9430.
  • Hea M. Tweedieverse - a unified statistical framework for differential analysis of multi-omics data. R package. 2021.
  • Team RC. R: a language and environment for statistical computing. Austria: R Foundation for Statistical Computing Vienna; 2020.
  • Brukner I, Longtin Y, Oughton M, Forgetta V, Dascal A. Assay for estimating total bacterial load: relative qPCR normalisation of bacterial load with associated clinical implications. Diagn Microbiol Infect Dis. 2015;83(1):1–6. doi:10.1016/j.diagmicrobio.2015.04.005.

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