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Research Paper

Microbiome function and neurodevelopment in Black infants: vitamin B12 emerges as a key factor

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Article: 2298697 | Received 08 Jun 2023, Accepted 20 Dec 2023, Published online: 01 Feb 2024

References

  • Hackman DA, Farah MJ, Meaney MJ. Socioeconomic status and the brain: mechanistic insights from human and animal research. Nat Rev Neurosci. 2010;11(9):651. doi:10.1038/nrn2897.
  • Keenan K, Gunthorpe D, Grace D. Parsing the relations between SES and stress reactivity: examining individual differences in neonatal stress response. Infant Behav Dev. 2007;30(1):134–27. doi:10.1016/j.infbeh.2006.08.001.
  • Wang S, Ryan CA, Boyaval P, Dempsey EM, Ross RP, Stanton C. Maternal vertical transmission affecting early-life microbiota development. Trends Microbiol. 2020;28(1):28–45. doi:10.1016/j.tim.2019.07.010.
  • Oliphant K, Lu J. Chapter 6 - neurodevelopment and the gut microbiome [Internet]. In: Claud Eeditor. The developing microbiome. Academic Press; 2020. pp. 115–143. [accessed 2022 Sep 16]. https://www.sciencedirect.com/science/article/pii/B9780128206027000064
  • Lu J, Claud EC. Connection between gut microbiome and brain development in preterm infants. Dev Psychobiol. 2019;61(5):739–751. doi:10.1002/dev.21806.
  • Pulikkan J, Mazumder A, Grace T. Role of the gut microbiome in autism spectrum disorders. Adv Exp Med Biol. 2019;1118:253–269.
  • Dam SA, Mostert JC, Szopinska-Tokov JW, Bloemendaal M, Amato M, Arias-Vasquez A. The role of the gut-brain axis in attention-deficit/Hyperactivity disorder. Gastroenterol Clin North Am. 2019;48(3):407–431. doi:10.1016/j.gtc.2019.05.001.
  • Bowyer RCE, Jackson MA, Le Roy CI, Ni Lochlainn M, Spector TD, Dowd JB, Steves CJ. Socioeconomic status and the gut microbiome: a TwinsUK cohort study. Microorganisms. 2019;7(1):17. doi:10.3390/microorganisms7010017.
  • Miller GE, Engen PA, Gillevet PM, Shaikh M, Sikaroodi M, Forsyth CB, Mutlu E, Keshavarzian A, Driks A. Lower neighborhood socioeconomic status associated with reduced diversity of the colonic microbiota in healthy adults. PLoS ONE. 2016;11(2):e0148952. doi:10.1371/journal.pone.0148952.
  • Lewis CR, Bonham KS, McCann SH, Volpe AR, D’Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, et al. Family SES is associated with the gut microbiome in infants and children. Microorganisms. 2021;9(8):1608. doi:10.3390/microorganisms9081608.
  • Keenan K, Hipwell AE, Class QA, Mbayiwa K. Extending the developmental origins of disease model: impact of preconception stress exposure on offspring neurodevelopment. Dev Psychobiol. 2018;60(7):753–764. doi:10.1002/dev.21773.
  • Pudell C, Vicente BA, Delattre AM, Carabelli B, Mori MA, Suchecki D, Machado RB, Zanata SM, Visentainer JV, de Oliveira Santos Junior O, et al. Fish oil improves anxiety-like, depressive-like and cognitive behaviors in olfactory bulbectomised rats. Eur J Neurosci. 2014;39(2):266–274. doi:10.1111/ejn.12406.
  • Feng Z, Zou X, Jia H, Li X, Zhu Z, Liu X, Bucheli P, Ballevre O, Hou Y, Zhang W, et al. Maternal docosahexaenoic acid feeding protects against impairment of learning and memory and oxidative stress in prenatally stressed rats: possible role of neuronal mitochondria metabolism. Antioxid Redox Signal. 2012;16(3):275–289. doi:10.1089/ars.2010.3750.
  • Division (DCD) DC. Who’s eligible for Medicaid? [Internet]. HHS.Gov12AD. [accessed 2023 Sep 13]. https://www.hhs.gov/answers/medicare-and-medicaid/who-is-eligible-for-medicaid/index.html
  • Linares A Chicago community area hardship index 2016-2020 [Internet]. ArcGis StoryMaps2022. [accessed 2023 Sep 13]. https://storymaps.arcgis.com/stories/da5601c3e0924e5ab3ee07ade9954f7a
  • Nathan RP, Adams C. Understanding central city hardship. Polit Sci Q. 1976;91(1):47–62. doi:10.2307/2149158.
  • Venkatramanan S, Armata IE, Strupp BJ, Finkelstein JL. Vitamin B-12 and cognition in Children123. Adv Nutr. 2016;7(5):879–888. doi:10.3945/an.115.012021.
  • O’Logbon J, Crook M, Steed D, Harrington DJ, Sobczyńska-Malefora A. Ethnicity influences total serum vitamin B12 concentration: a study of black, Asian and white patients in a primary care setting. J Clin Pathol. 2022;75(9):598–604. doi:10.1136/jclinpath-2021-207519.
  • Bailey RL, Carmel R, Green R, Pfeiffer CM, Cogswell ME, Osterloh JD, Sempos CT, Yetley EA. Monitoring of vitamin B-12 nutritional status in the United States by using plasma methylmalonic acid and serum vitamin B-121234. Am J Clin Nutr. 2011;94(2):552–561. doi:10.3945/ajcn.111.015222.
  • Degnan PH, Taga ME, Goodman AL. Vitamin B12 as a modulator of gut microbial ecology. Cell Metab. 2014;20(5):769–778. doi:10.1016/j.cmet.2014.10.002.
  • Rowley CA, Kendall MM, Leong JM. To B12 or not to B12: five questions on the role of cobalamin in host-microbial interactions. PLoS Pathog. 2019;15(1):e1007479. doi:10.1371/journal.ppat.1007479.
  • Allen RH, Stabler SP. Identification and quantitation of cobalamin and cobalamin analogues in human feces. Am J Clin Nutr. 2008;87(5):1324–1335. doi:10.1093/ajcn/87.5.1324.
  • Soto-Martin EC, Warnke I, Farquharson FM, Christodoulou M, Horgan G, Derrien M, Faurie J-M, Flint HJ, Duncan SH, Louis P, et al. Vitamin biosynthesis by human gut butyrate-producing bacteria and cross-feeding in synthetic microbial communities. mBio. 2020;11(4):e00886–20. doi:10.1128/mBio.00886-20.
  • Torrents E. Ribonucleotide reductases: essential enzymes for bacterial life. Front Cell Infect Microbiol [Internet]. 2014;4. 10.3389/fcimb.2014.00052
  • Dreux N, Del M Cendra M, Massier S, Darfeuille-Michaud A, Barnich N, Torrents E, McCormick BA. Ribonucleotide Reductase NrdR as a Novel Regulator for Motility and Chemotaxis during Adherent-Invasive Escherichia coli Infection. Infect Immun. 2015;83(4):1305–1317. doi:10.1128/IAI.02772-14.
  • Tran S-S, Mohajeri MH. The role of gut bacterial metabolites in brain development, aging and disease. Nutrients. 2021;13(3):732. doi:10.3390/nu13030732.
  • Quan L, Yi J, Zhao Y, Zhang F, Shi X-T, Feng Z, Miller HL. Plasma trimethylamine N-oxide, a gut microbe-generated phosphatidylcholine metabolite, is associated with autism spectrum disorders. Neurotoxicology. 2020;76:93–98. doi:10.1016/j.neuro.2019.10.012.
  • Eicher TP, Mohajeri MH. Overlapping mechanisms of action of brain-active bacteria and bacterial metabolites in the pathogenesis of common brain diseases. Nutrients. 2022;14(13):2661. doi:10.3390/nu14132661.
  • Fattorusso A, Di Genova L, Dell’isola GB, Mencaroni E, Esposito S. Autism spectrum disorders and the gut microbiota. Nutrients. 2019;11(3):521. doi:10.3390/nu11030521.
  • Mandal R, Cano R, Davis CD, Hayashi D, Jackson SA, Jones CM, Lampe JW, Latulippe ME, Lin NJ, Lippa KA, et al. Workshop report: toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements. Metabolomics. 2020;16(11):119. doi:10.1007/s11306-020-01744-5.
  • Verbeke KA, Boobis AR, Chiodini A, Edwards CA, Franck A, Kleerebezem M, Nauta A, Raes J, van Tol EAF, Tuohy KM. Towards microbial fermentation metabolites as markers for health benefits of prebiotics. Nutr Res Rev. 2015;28(1):42–66. doi:10.1017/S0954422415000037.
  • Cardoso FL, Herz J, Fernandes A, Rocha J, Sepodes B, Brito MA, McGavern DB, Brites D. Systemic inflammation in early neonatal mice induces transient and lasting neurodegenerative effects. J Neuroinflammation. 2015;12(1):82. doi:10.1186/s12974-015-0299-3.
  • Cao X, Liu K, Liu J, Liu Y-W, Xu L, Wang H, Zhu Y, Wang P, Li Z, Wen J, et al. Dysbiotic gut microbiota and dysregulation of cytokine profile in children and teens with autism spectrum disorder. Front Neurosci [Internet]. 2021;15. 10.3389/fnins.2021.635925
  • Jiang NM, Tofail F, Moonah SN, Scharf RJ, Taniuchi M, Ma JZ, Hamadani JD, Gurley ES, Houpt ER, Azziz-Baumgartner E, et al. Febrile illness and pro-inflammatory cytokines are associated with lower neurodevelopmental scores in Bangladeshi infants living in poverty. BMC Pediatr. 2014;14(1):50. doi:10.1186/1471-2431-14-50.
  • Lee SE, West KP, Cole RN, Schulze KJ, Wu L-F, Yager JD, Groopman J, Christian P. General intelligence is associated with subclinical inflammation in Nepalese children: a population-based plasma proteomics study. Brain Behav Immun. 2016;56:253–263. doi:10.1016/j.bbi.2016.03.023.
  • Pham VT, Dold S, Rehman A, Bird JK, Steinert RE. Vitamins, the gut microbiome and gastrointestinal health in humans. Nutr Res. 2021;95:35–53. doi:10.1016/j.nutres.2021.09.001.
  • Dahl WJ, Rivero Mendoza D, Lambert JM. Chapter eight - diet, nutrients and the microbiome [Internet]. In: Sun Jeditor. Progress in molecular biology and translational science. Academic Press; 2020; [accessed 2022 Oct 12]. pp. 237–263. https://www.sciencedirect.com/science/article/pii/S1877117320300508
  • Han S, Wu L, Wang W, Li N, Wu X. Trends in dietary nutrients by demographic characteristics and BMI among US adults, 2003–2016. Nutrients. 2019;11(11):2617. doi:10.3390/nu11112617.
  • Selma-Royo M, García-Mantrana I, Calatayud M, Parra-Llorca A, Martínez-Costa C, Collado MC. Maternal diet during pregnancy and intestinal markers are associated with early gut microbiota. Eur J Nutr. 2021;60(3):1429–1442. doi:10.1007/s00394-020-02337-7.
  • Tamana SK, Tun HM, Konya T, Chari RS, Field CJ, Guttman DS, Becker AB, Moraes TJ, Turvey SE, Subbarao P, et al. Bacteroides-dominant gut microbiome of late infancy is associated with enhanced neurodevelopment. Gut Microbes. 2021;13(1):1–17. doi:10.1080/19490976.2021.1930875.
  • Global, regional, and national burden of 12 mental disorders in 204 countries and territories, 1990–2019: a systematic analysis for the global burden of disease study 2019. Lancet Psychiatry. 2022;9(2):137–150. doi:10.1016/S2215-0366(21)00395-3.
  • Zablotsky B, Black LI, Maenner MJ, Schieve LA, Danielson ML, Bitsko RH, Blumberg SJ, Kogan MD, Boyle CA. Prevalence and trends of developmental disabilities among children in the United States: 2009–2017. Pediatrics. 2019;144(4):e20190811. doi:10.1542/peds.2019-0811.
  • Fox M, Lee SM, Wiley KS, Lagishetty V, Sandman CA, Jacobs JP, Glynn LM. Development of the infant gut microbiome predicts temperament across the first year of life. Dev Psychopathol. 2021;34(5):1914–1925. doi:10.1017/S0954579421000456.
  • Aatsinki A-K, Lahti L, Uusitupa H-M, Munukka E, Keskitalo A, Nolvi S, O’Mahony S, Pietilä S, Elo LL, Eerola E, et al. Gut microbiota composition is associated with temperament traits in infants. Brain Behav Immun. 2019;80:849–858. doi:10.1016/j.bbi.2019.05.035.
  • Thurstans S, Opondo C, Seal A, Wells JC, Khara T, Dolan C, Briend A, Myatt M, Garenne M, Mertens A, et al. Understanding sex differences in childhood undernutrition: a narrative review. Nutrients. 2022;14(5):948. doi:10.3390/nu14050948.
  • Barrera CM, Hamner HC, Perrine CG, Scanlon KS. Timing of introduction of complementary foods to US infants, national health and nutrition examination survey 2009–2014. J Acad Nutr Diet. 2018;118(3):464–470. doi:10.1016/j.jand.2017.10.020.
  • Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci. 2011;108(supplement_1):4578–4585. doi:10.1073/pnas.1000081107.
  • Differding MK, Benjamin-Neelon SE, Hoyo C, Østbye T, Mueller NT. Timing of complementary feeding is associated with gut microbiota diversity and composition and short chain fatty acid concentrations over the first year of life. BMC Microbiol. 2020;20(1):56. doi:10.1186/s12866-020-01723-9.
  • Laursen MF. Gut microbiota development: influence of diet from infancy to toddlerhood. Ann Nutr Metab. 2021;77(Suppl. 3):21–34. doi:10.1159/000517912.
  • 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.
  • Guzior DV, Quinn RA. Review: microbial transformations of human bile acids. Microbiome. 2021;9(1):140. doi:10.1186/s40168-021-01101-1.
  • Sabater C, Molinero-García N, Castro-Bravo N, Diez-Echave P, Hidalgo-García L, Delgado S, Sánchez B, Gálvez J, Margolles A, Ruas-Madiedo P. Exopolysaccharide producing bifidobacterium animalis subsp. lactis strains modify the intestinal microbiota and the plasmatic cytokine levels of BALB/c mice according to the type of polymer synthesized. Front Microbiol. 2020;11:601233. doi:10.3389/fmicb.2020.601233.
  • Bleau C, Monges A, Rashidan K, Laverdure J-P, Lacroix M, Van Calsteren M-R, Millette M, Savard R, Lamontagne L. Intermediate chains of exopolysaccharides from Lactobacillus rhamnosus RW-9595M increase IL-10 production by macrophages. J Appl Microbiol. 2010;108(2):666–675. doi:10.1111/j.1365-2672.2009.04450.x.
  • Di Lorenzo F, Pither MD, Martufi M, Scarinci I, Guzmán-Caldentey J, Łakomiec E, Jachymek W, Bruijns SCM, Santamaría SM, Frick J-S, et al. Pairing bacteroides vulgatus LPS structure with its immunomodulatory effects on human cellular models. ACS Cent Sci. 2020;6(9):1602–1616. doi:10.1021/acscentsci.0c00791.
  • Kaiser JC, Heinrichs DE, Garsin DA. Branching out: alterations in bacterial physiology and virulence due to branched-chain amino acid deprivation. mBio. 2018;9(5):e01188–18. doi:10.1128/mBio.01188-18.
  • Mijailovic NR, Vesic K, Borovcanin MM. The influence of serum uric acid on the brain and cognitive dysfunction. Front Psychiatry. 2022;13:828476. doi:10.3389/fpsyt.2022.828476.
  • Baronio D, Gonchoroski T, Castro K, Zanatta G, Gottfried C, Riesgo R. Histaminergic system in brain disorders: lessons from the translational approach and future perspectives. Ann Gen Psychiatry. 2014;13(1):34. doi:10.1186/s12991-014-0034-y.
  • Thalacker-Mercer AE, Gheller ME. Benefits and adverse effects of histidine supplementation. J Nutr. 2020;150:2588S–2592S. doi:10.1093/jn/nxaa229.
  • Clayton TA. Metabolic differences underlying two distinct rat urinary phenotypes, a suggested role for gut microbial metabolism of phenylalanine and a possible connection to autism. FEBS Lett. 2012;586(7):956–961. doi:10.1016/j.febslet.2012.01.049.
  • Yap IKS, Angley M, Veselkov KA, Holmes E, Lindon JC, Nicholson JK. Urinary metabolic phenotyping differentiates children with autism from their unaffected siblings and age-matched controls. J Proteome Res. 2010;9(6):2996–3004. doi:10.1021/pr901188e.
  • Xiong X, Liu D, Wang Y, Zeng T, Peng Y. Urinary 3-(3-hydroxyphenyl)-3-hydroxypropionic acid, 3-hydroxyphenylacetic acid, and 3-hydroxyhippuric acid are elevated in children with autism spectrum disorders. Biomed Res Int. 2016;2016:9485412. doi:10.1155/2016/9485412.
  • Shaw W. Increased urinary excretion of a 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), an abnormal phenylalanine metabolite of clostridia spp. In the gastrointestinal tract, in urine samples from patients with autism and schizophrenia. Nutr Neurosci. 2010;13(3):135–143. doi:10.1179/147683010X12611460763968.
  • Round JL, Lee SM, Li J, Tran G, Jabri B, Chatila TA, Mazmanian SK. The toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Sci. 2011;332(6032):974–977. doi:10.1126/science.1206095.
  • Saito S, Okuno A, Cao D-Y, Peng Z, Wu H-Y, Lin S-H. Bacterial Lipoteichoic Acid Attenuates Toll-Like Receptor Dependent Dendritic Cells Activation and Inflammatory Response. Pathogens. 2020;9(10):825. doi:10.3390/pathogens9100825.
  • Nigou J, Gilleron M, Puzo G. Lipoarabinomannans: from structure to biosynthesis. Biochimie. 2003;85(1–2):153–166. doi:10.1016/S0300-9084(03)00048-8.
  • Alamoudi MU, Hosie S, Shindler AE, Wood JL, Franks AE, Hill-Yardin EL. Comparing the gut microbiome in autism and preclinical models: a systematic review. Front Cell Infect Microbiol. 2022;12:905841. doi:10.3389/fcimb.2022.905841.
  • Sen P, Sherwin E, Sandhu K, Bastiaanssen TFS, Moloney GM, Golubeva A, Fitzgerald P, Paula Ventura Da Silva A, Chruścicka-Smaga B, Olavarría-Ramírez L, et al. The live biotherapeutic blautia stercoris MRx0006 attenuates social deficits, repetitive behaviour, and anxiety-like behaviour in a mouse model relevant to autism. Brain Behav Immun. 2022;106:115–126. doi:10.1016/j.bbi.2022.08.007.
  • Yang J, Zheng P, Li Y, Wu J, Tan X, Zhou J, Sun Z, Chen X, Zhang G, Zhang H, et al. Landscapes of bacterial and metabolic signatures and their interaction in major depressive disorders. Sci Adv. 2020;6(49):eaba8555. doi:10.1126/sciadv.aba8555.
  • Lu S, Yang Y, Xu Q, Wang S, Yu J, Zhang B, Wang Z, Zhang Y, Lu W, Hong K. Gut microbiota and targeted biomarkers analysis in patients with cognitive impairment. Front Neurol. 2022;13:834403. doi:10.3389/fneur.2022.834403.
  • Qi C, Zhou J, Tu H, Tu R, Chang H, Chen J, Li D, Sun J, Yu R. Lactation-dependent vertical transmission of natural probiotics from the mother to the infant gut through breast milk. Food Funct. 2022;13(1):304–315. doi:10.1039/D1FO03131G.
  • Guzzardi MA, Ederveen THA, Rizzo F, Weisz A, Collado MC, Muratori F, Gross G, Alkema W, Iozzo P. Maternal pre-pregnancy overweight and neonatal gut bacterial colonization are associated with cognitive development and gut microbiota composition in pre-school-age offspring. Brain Behav Immun. 2022;100:311–320. doi:10.1016/j.bbi.2021.12.009.
  • Michalec D. Bayley scales of infant development In: Internet. ThirdGoldstein S Naglieri Jeditors. Encyclopedia of child behavior and development. Boston, MA: Springer US;2011. pp. 215–215. 10.1007/978-0-387-79061-9_295
  • Freeman Duncan A, Watterberg KL, Nolen TL, Vohr BR, Adams-Chapman I, Das A, Lowe J. Effect of ethnicity and race on cognitive and language testing at age 18-22 months in extremely preterm infants. J Pediatr. 2012;160(6):966–971.e2. doi:10.1016/j.jpeds.2011.12.009.
  • L’Hotta AJ, Hoyt CR, Lindsey T, Abel RA, Chang C-H, King AA. Validation of the fine motor subtest of the bayley-III with children with sickle cell disease using Rasch analysis. Child Care Health Dev. 2020;46(5):576–584. doi:10.1111/cch.12795.
  • Hess CR, Papas MA, Black MM. Use of the bayley infant neurodevelopmental screener with an environmental risk group. J Pediatr Psychol. 2004;29(5):321–330. doi:10.1093/jpepsy/jsh036.
  • Bates JE, Freeland CA, Lounsbury ML. Measurement of infant difficultness. Child Dev. 1979;50(3):794–803. doi:10.2307/1128946.
  • Joseph HM, McKone KMP, Molina BSG, Shaw DS. Maternal parenting and toddler temperament: predictors of early school age attention-deficit/Hyperactivity disorder-related behaviors. Res Child Adolesc Psychopathol. 2021;49(6):763–773. doi:10.1007/s10802-021-00778-0.
  • Putnam SP, Helbig AL, Gartstein MA, Rothbart MK, Leerkes E. Development and assessment of short and very short forms of the infant behavior questionnaire–revised. J Pers Assess. 2014;96(4):445–458. doi:10.1080/00223891.2013.841171.
  • Tronick E, Als H, Adamson L, Wise S, Brazelton TB. The infant’s response to entrapment between contradictory messages in face-to-face interaction. J Am Acad Child Psychiatry. 1978;17(1):1–13. doi:10.1016/S0002-7138(09)62273-1.
  • Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, et al. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems. 2016;1(1). doi:10.1128/mSystems.00009-15.
  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6(8):1621–1624. doi:10.1038/ismej.2012.8.
  • Oliphant K, Cruz Ayala W, Ilyumzhinova R, Mbayiwa K, Sroka A, Xie B, Andrews B, Keenan K, Claud EC [dataset] Microbiome function and neurodevelopment in black infants: vitamin B12 biosynthesis emerges as a key factor [Internet]. NCBI SRA2022; https://www.ncbi.nlm.nih.gov/bioproject/895372
  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi:10.1038/nmeth.3869.
  • Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–857. doi:10.1038/s41587-019-0209-9.
  • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(D1):D590–6. doi:10.1093/nar/gks1219.
  • Hsieh TC, Ma KH, Chao A, McInerny G. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol Evol. 2016;7(12):1451–1456. doi:10.1111/2041-210X.12613.
  • Holmes I, Harris K, Quince C, Gilbert JA. Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics. PLoS ONE. 2012;7(2):e30126. doi:10.1371/journal.pone.0030126.
  • McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C, Hancock J. bioBakery: a meta’omic analysis environment. Bioinforma Oxf Engl. 2018;34(7):1235–1237. doi:10.1093/bioinformatics/btx754.
  • Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, Bourexis D, Brister JR, Bryant SH, Canese K, et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2018;46(D1):D8–13. doi:10.1093/nar/gkx1095.
  • Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, Leipe D, Mcveigh R, O’Neill K, Robbertse B, et al. NCBI taxonomy: a comprehensive update on curation, resources and tools. Database. 2020;2020:baaa062. doi:10.1093/database/baaa062.
  • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27–30. doi:10.1093/nar/28.1.27.
  • Haak BW, Littmann ER, Chaubard J-L, Pickard AJ, Fontana E, Adhi F, Gyaltshen Y, Ling L, Morjaria SM, Peled JU, et al. Impact of gut colonization with butyrate-producing microbiota on respiratory viral infection following allo-HCT. Blood. 2018;131:2978–2986. doi:10.1182/blood-2018-01-828996.
  • Shan J, Peng L, Qian W, Xie T, Kang A, Gao B, Di L. Integrated serum and fecal metabolomics study of collagen-induced arthritis rats and the therapeutic effects of the zushima tablet. Front Pharmacol [Internet]. 2018;9. 10.3389/fphar.2018.00891
  • Fiehn O. Metabolomics by gas chromatography–mass spectrometry: combined targeted and untargeted profiling. Curr Protoc Mol Biol. 2016;114(1):30.4.1–30.4.32. doi:10.1002/0471142727.mb3004s114.
  • Gómez C, Stücheli S, Kratschmar DV, Bouitbir J, Odermatt A. Development and validation of a highly sensitive LC-MS/MS method for the analysis of bile acids in serum, plasma, and liver tissue samples. Metabolites. 2020;10(7):282. doi:10.3390/metabo10070282.