Mitsuoka T. Intestinal flora and aging. Nutr Rev. 1992;50(12):438–46.
CAS
PubMed
Google Scholar
Biagi E, et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One. 2010;5(5):e10667.
PubMed
PubMed Central
Google Scholar
Mueller S, et al. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol. 2006;72(2):1027–33.
CAS
PubMed
PubMed Central
Google Scholar
Hayashi H, et al. Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP. Microbiol Immunol. 2003;47(8):557–70.
CAS
PubMed
Google Scholar
Mariat D, et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol. 2009;9:123.
CAS
PubMed
PubMed Central
Google Scholar
Rajilic-Stojanovic M, et al. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol. 2009;11(7):1736–51.
CAS
PubMed
PubMed Central
Google Scholar
Woodmansey EJ, et al. Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects. Appl Environ Microbiol. 2004;70(10):6113–22.
CAS
PubMed
PubMed Central
Google Scholar
Bartosch S, et al. Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota. Appl Environ Microbiol. 2004;70(6):3575–81.
CAS
PubMed
PubMed Central
Google Scholar
van Tongeren SP, et al. Fecal microbiota composition and frailty. Appl Environ Microbiol. 2005;71(10):6438–42.
PubMed
PubMed Central
Google Scholar
Tiihonen K, et al. The effect of ageing with and without non-steroidal anti-inflammatory drugs on gastrointestinal microbiology and immunology. Br J Nutr. 2008;100(1):130–7.
CAS
PubMed
Google Scholar
Makivuokko H, et al. The effect of age and non-steroidal anti-inflammatory drugs on human intestinal microbiota composition. Br J Nutr. 2010;103(2):227–34.
PubMed
Google Scholar
Tiihonen K, Ouwehand AC, Rautonen N. Human intestinal microbiota and healthy ageing. Ageing Res Rev. 2010;9(2):107–16.
PubMed
Google Scholar
Shin JH, High KP, Warren CA. Older is not wiser, immunologically speaking: effect of aging on host response to Clostridium difficile infections. J Gerontol A Biol Sci Med Sci. 2016;71(7):916–22.
CAS
PubMed
PubMed Central
Google Scholar
Drekonja D, et al. Fecal microbiota transplantation for Clostridium difficile infection: a systematic review. Ann Intern Med. 2015;162(9):630–8.
PubMed
Google Scholar
Konturek PC, et al. Emerging role of fecal microbiota therapy in the treatment of gastrointestinal and extra-gastrointestinal diseases. J Physiol Pharmacol. 2015;66(4):483–91.
CAS
PubMed
Google Scholar
Rampelli S, et al. Functional metagenomic profiling of intestinal microbiome in extreme ageing. Aging (Albany NY). 2013;5(12):902–12.
CAS
Google Scholar
Langille MG, et al. Microbial shifts in the aging mouse gut. Microbiome. 2014;2(1):50.
PubMed
PubMed Central
Google Scholar
Elderman M, et al. The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice. PLoS One. 2017;12(9):e0184274.
PubMed
PubMed Central
Google Scholar
Sovran B, et al. Age-associated impairment of the mucus barrier function is associated with profound changes in microbiota and immunity. Sci Rep. 2019;9(1):1437.
PubMed
PubMed Central
Google Scholar
Kobayashi A, et al. The functional maturation of M cells is dramatically reduced in the Peyer’s patches of aged mice. Mucosal Immunol. 2013;6(5):1027–37.
CAS
PubMed
PubMed Central
Google Scholar
Arike L, Holmen-Larsson J, Hansson GC. Intestinal Muc2 mucin O-glycosylation is affected by microbiota and regulated by differential expression of glycosyltranferases. Glycobiology. 2017;27(4):318–28.
CAS
PubMed
PubMed Central
Google Scholar
Arike L, Hansson GC. The densely O-glycosylated MUC2 mucin protects the intestine and provides food for the commensal bacteria. J Mol Biol. 2016;428(16):3221–9.
CAS
PubMed
PubMed Central
Google Scholar
Johansson ME, et al. Normalization of host intestinal mucus layers requires long-term microbial colonization. Cell Host Microbe. 2015;18(5):582–92.
CAS
PubMed
PubMed Central
Google Scholar
van Beek AA, et al. Supplementation with Lactobacillus plantarum WCFS1 prevents decline of mucus barrier in colon of accelerated aging Ercc1(-/Δ7) mice. Front Immunol. 2016;7:408.
PubMed
PubMed Central
Google Scholar
van der Lugt B, et al. Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1 (-/Δ7) mice. Immun Ageing. 2019;16:6.
PubMed
PubMed Central
Google Scholar
Karav S, Casaburi G, Frese SA. Reduced colonic mucin degradation in breastfed infants colonized by Bifidobacterium longum subsp. infantis EVC001. FEBS Open Bio. 2018;8(10):1649–57.
CAS
PubMed
PubMed Central
Google Scholar
Schroeder BO, et al. Bifidobacteria or fiber protects against diet-induced microbiota-mediated colonic mucus deterioration. Cell Host Microbe. 2018;23(1):27–40 e7.
CAS
PubMed
Google Scholar
Thevaranjan N, et al. Age-associated microbial dysbiosis promotes intestinal permeability, systemic inflammation, and macrophage dysfunction. Cell Host Microbe. 2017;21(4):455–66 e4.
CAS
PubMed
PubMed Central
Google Scholar
Maijo M, et al. Nutrition, diet and immunosenescence. Mech Ageing Dev. 2014;136-137:116–28.
CAS
PubMed
Google Scholar
Vasto S, et al. Inflammatory networks in ageing, age-related diseases and longevity. Mech Ageing Dev. 2007;128(1):83–91.
CAS
PubMed
Google Scholar
Sarkar D, Fisher PB. Molecular mechanisms of aging-associated inflammation. Cancer Lett. 2006;236(1):13–23.
CAS
PubMed
Google Scholar
Butto LF, Haller D. Dysbiosis in intestinal inflammation: cause or consequence. Int J Med Microbiol. 2016;306(5):302–9.
PubMed
Google Scholar
Carding S, et al. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis. 2015;26:26191.
PubMed
Google Scholar
Buford TW. (Dis)Trust your gut: the gut microbiome in age-related inflammation, health, and disease. Microbiome. 2017;5(1):80.
PubMed
PubMed Central
Google Scholar
Azcarate-Peril MA, et al. Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism. Applied and Environmental Microbiology. 2008;74(15):4610–25.
CAS
PubMed
PubMed Central
Google Scholar
Vandenplas Y, Zakharova I, Dmitrieva Y. Oligosaccharides in infant formula: more evidence to validate the role of prebiotics. Br J Nutr. 2015;113(9):1339–44.
CAS
PubMed
Google Scholar
Akkerman R, Faas MM, de Vos P. Non-digestible carbohydrates in infant formula as substitution for human milk oligosaccharide functions: Effects on microbiota and gut maturation. Crit Rev Food Sci Nutr. 2019;59(9):1486–97.
CAS
PubMed
Google Scholar
Bhatia S, et al. Galacto-oligosaccharides may directly enhance intestinal barrier function through the modulation of goblet cells. Mol Nutr Food Res. 2015;59(3):566–73.
CAS
PubMed
Google Scholar
Akbari P, et al. Galacto-oligosaccharides protect the intestinal barrier by maintaining the tight junction network and modulating the inflammatory responses after a challenge with the mycotoxin deoxynivalenol in human Caco-2 cell monolayers and B6C3F1 mice. J Nutr. 2015;145(7):1604–13.
CAS
PubMed
Google Scholar
Alizadeh A, et al. The piglet as a model for studying dietary components in infant diets: effects of galacto-oligosaccharides on intestinal functions. Br J Nutr. 2016;115(4):605–18.
CAS
PubMed
Google Scholar
Davis LM, et al. Barcoded pyrosequencing reveals that consumption of galactooligosaccharides results in a highly specific bifidogenic response in humans. PLoS One. 2011;6(9):e25200.
CAS
PubMed
PubMed Central
Google Scholar
Scalabrin DM, et al. New prebiotic blend of polydextrose and galacto-oligosaccharides has a bifidogenic effect in young infants. J Pediatr Gastroenterol Nutr. 2012;54(3):343–52.
CAS
PubMed
Google Scholar
Salvini F, et al. A specific prebiotic mixture added to starting infant formula has long-lasting bifidogenic effects. J Nutr. 2011;141(7):1335–9.
CAS
PubMed
PubMed Central
Google Scholar
Rowland IR, Tanaka R. The effects of transgalactosylated oligosaccharides on gut flora metabolism in rats associated with a human faecal microflora. J Appl Bacteriol. 1993;74(6):667–74.
CAS
PubMed
Google Scholar
Monteagudo-Mera A, et al. High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome. Benef Microbes. 2016;3:1–18.
Google Scholar
Azcarate Peril MA, et al. Microbiome alterations of lactose intolerant individuals in response to dietary intervention with galacto-oligosaccharides may help negate symptoms of lactose intolerance. Gastroenterology. 2013;144(5):S–893.
Google Scholar
Azcarate-Peril MA, et al. Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals. Proc Natl Acad Sci U S A. 2017;114(3):E367–75.
CAS
PubMed
PubMed Central
Google Scholar
Vulevic J, et al. Modulation of the fecal microflora profile and immune function by a novel trans-galactooligosaccharide mixture (B-GOS) in healthy elderly volunteers. Am J Clin Nutr. 2008;88(5):1438–46.
CAS
PubMed
Google Scholar
Dagher SF, Azcarate-Peril MA, Bruno-Barcena JM. Heterologous expression of a bioactive beta-hexosyltransferase, an enzyme producer of prebiotics, from Sporobolomyces singularis. Appl Environ Microbiol. 2013;79(4):1241–9.
CAS
PubMed
PubMed Central
Google Scholar
Giarratano A, Green SE, Nicolau DP. Review of antimicrobial use and considerations in the elderly population. Clin Interv Aging. 2018;13:657–67.
CAS
PubMed
PubMed Central
Google Scholar
Van Boeckel TP, et al. Global trends in antimicrobial use in food animals. Proc Natl Acad Sci U S A. 2015;112(18):5649–54.
PubMed
PubMed Central
Google Scholar
Dethlefsen, L. and D.A. Relman, Microbes and Health Sackler Colloquium: incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A.
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4554–61.
CAS
PubMed
Google Scholar
Williamson IA, et al. A high-throughput organoid microinjection platform to study gastrointestinal microbiota and luminal physiology. Cell Mol Gastroenterol Hepatol. 2018;6(3):301–19.
PubMed
PubMed Central
Google Scholar
Vulevic J, et al. Influence of galacto-oligosaccharide mixture (B-GOS) on gut microbiota, immune parameters and metabonomics in elderly persons. Br J Nutr. 2015;114(4):586–95.
CAS
PubMed
Google Scholar
Arnold JW, et al. Prebiotics for lactose intolerance: variability in galacto-oligosaccharide utilization by intestinal Lactobacillus rhamnosus. Nutrients. 2018;10(10):1517. https://doi.org/10.3390/nu10101517.
Article
CAS
PubMed Central
Google Scholar
Rios-Covian D, et al. Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis. FEMS Microbiol Lett. 2015;362(21):fnv176. https://doi.org/10.1093/femsle/fnv176. Epub 2015 Sep 28.
Riviere A, et al. Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut. Front Microbiol. 2016;7:979.
PubMed
PubMed Central
Google Scholar
Sivaprakasam S, Prasad PD, Singh N. Benefits of short-chain fatty acids and their receptors in inflammation and carcinogenesis. Pharmacol Ther. 2016;164:144–51. https://doi.org/10.1016/j.pharmthera.2016.04.007. Epub 2016 Apr 23.
Lewis K, et al. Enhanced translocation of bacteria across metabolically stressed epithelia is reduced by butyrate. Inflamm Bowel Dis. 2010;16(7):1138–48.
PubMed
Google Scholar
Gaudier E, et al. Butyrate regulation of glycosylation-related gene expression: evidence for galectin-1 upregulation in human intestinal epithelial goblet cells. Biochem Biophys Res Commun. 2004;325(3):1044–51.
CAS
PubMed
Google Scholar
Renes IB, et al. Epithelial proliferation, cell death, and gene expression in experimental colitis: alterations in carbonic anhydrase I, mucin MUC2, and trefoil factor 3 expression. Int J Colorectal Dis. 2002;17(5):317–26.
PubMed
Google Scholar
Aihara E, Engevik KA, Montrose MH. Trefoil factor peptides and gastrointestinal function. Annu Rev Physiol. 2017;79:357–80.
CAS
PubMed
Google Scholar
Hogan SP, et al. Resistin-like molecule beta regulates innate colonic function: barrier integrity and inflammation susceptibility. J Allergy Clin Immunol. 2006;118(1):257–68.
CAS
PubMed
PubMed Central
Google Scholar
Bouchlaka MN, et al. Aging predisposes to acute inflammatory induced pathology after tumor immunotherapy. J Exp Med. 2013;210(11):2223–37.
CAS
PubMed
PubMed Central
Google Scholar
Starr ME, et al. Age-associated increase in cytokine production during systemic inflammation-II: the role of IL-1β in age-dependent IL-6 upregulation in adipose tissue. J Gerontol A Biol Sci Med Sci. 2015;70(12):1508–15.
CAS
PubMed
Google Scholar
Szklarczyk D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–13.
CAS
PubMed
Google Scholar
Metsalu T, Vilo J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 2015;43(W1):W566–70.
CAS
PubMed
PubMed Central
Google Scholar
Laaf D, et al. Galectin-carbohydrate interactions in biomedicine and biotechnology. Trends Biotechnol. 2019;37(4):402–15.
CAS
PubMed
Google Scholar
Li FY, et al. Galectins in host defense against microbial infections. Adv Exp Med Biol. 2020;1204:141–67.
CAS
PubMed
Google Scholar
Jones RM, Neish AS. Redox signaling mediated by the gut microbiota. Free Radic Biol Med. 2017;105:41–7.
CAS
PubMed
Google Scholar
Clapham DE, Runnels LW, Strubing C. The TRP ion channel family. Nat Rev Neurosci. 2001;2(6):387–96.
CAS
PubMed
Google Scholar
Williamson IT, et al. A high-throughput organoid microinjection platform to study gastrointestinal microbiota and luminal physiology. Cell Mol Gastroenterol Hepatol. 2018;6(3):–301, 319.
Shoaf K, et al. Prebiotic galactooligosaccharides reduce adherence of enteropathogenic Escherichia coli to tissue culture cells. Infection and Immunity. 2006;74(12):6920–8.
CAS
PubMed
PubMed Central
Google Scholar
Zhao S, et al. Akkermansia muciniphila improves metabolic profiles by reducing inflammation in chow diet-fed mice. J Mol Endocrinol. 2017;58(1):1–14.
PubMed
Google Scholar
Collado MC, et al. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol. 2007;73(23):7767–70.
CAS
PubMed
PubMed Central
Google Scholar
Nicoletti C. Age-associated changes of the intestinal epithelial barrier: local and systemic implications. Expert Rev Gastroenterol Hepatol. 2015;9(12):1467–9.
CAS
PubMed
Google Scholar
Zwielehner J, et al. Combined PCR-DGGE fingerprinting and quantitative-PCR indicates shifts in fecal population sizes and diversity of Bacteroides, bifidobacteria and Clostridium cluster IV in institutionalized elderly. Exp Gerontol. 2009;44(6-7):440–6.
CAS
PubMed
Google Scholar
Raul F, et al. Age related increase of brush border enzyme activities along the small intestine. Gut. 1988;29(11):1557–63.
CAS
PubMed
PubMed Central
Google Scholar
Lee MF, et al. Total intestinal lactase and sucrase activities are reduced in aged rats. J Nutr. 1997;127(7):1382–7.
CAS
PubMed
Google Scholar
Matsuki T, et al. Infant formula with galacto-oligosaccharides (OM55N) stimulates the growth of indigenous bifidobacteria in healthy term infants. Benef Microbes. 2016;7(4):453–61.
CAS
PubMed
Google Scholar
So D, et al. Dietary fiber intervention on gut microbiota composition in healthy adults: a systematic review and meta-analysis. Am J Clin Nutr. 2018;107(6):965–83.
PubMed
Google Scholar
Szklany K, et al. Supplementation of dietary non-digestible oligosaccharides from birth onwards improve social and reduce anxiety-like behaviour in male BALB/c mice. Nutr Neurosci. 2019:1–15.
Cheng W, et al. Effect of functional oligosaccharides and ordinary dietary fiber on intestinal microbiota diversity. Front Microbiol. 2017;8:1750.
PubMed
PubMed Central
Google Scholar
Chen X, et al. A mouse model of Clostridium difficile-associated disease. Gastroenterology. 2008;135(6):1984–92.
PubMed
Google Scholar
Reikvam DH, et al. Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression. PLoS One. 2011;6(3):e17996.
CAS
PubMed
PubMed Central
Google Scholar
Zimmermann P, Curtis N. The effect of antibiotics on the composition of the intestinal microbiota - a systematic review. J Infect. 2019;79(6):471–89.
PubMed
Google Scholar
Barbut F, Meynard JL. Managing antibiotic associated diarrhoea. BMJ. 2002;324(7350):1345–6.
PubMed
PubMed Central
Google Scholar
Ladirat SE, et al. Impact of galacto-oligosaccharides on the gut microbiota composition and metabolic activity upon antibiotic treatment during in vitro fermentation. FEMS Microbiol Ecol. 2014;87(1):41–51.
CAS
PubMed
Google Scholar
Kudryavtseva AV, et al. Mitochondrial dysfunction and oxidative stress in aging and cancer. Oncotarget. 2016;7(29):44879–905.
PubMed
PubMed Central
Google Scholar
Vartak R, Porras CA, Bai Y. Respiratory supercomplexes: structure, function and assembly. Protein Cell. 2013;4(8):582–90.
CAS
PubMed
PubMed Central
Google Scholar
Arslanoglu S, et al. Early dietary intervention with a mixture of prebiotic oligosaccharides reduces the incidence of allergic manifestations and infections during the first two years of life. J Nutr. 2008;138(6):1091–5.
CAS
PubMed
Google Scholar
Schouten B, et al. Oligosaccharide-induced whey-specific CD25(+) regulatory T-cells are involved in the suppression of cow milk allergy in mice. J Nutr. 2010;140(4):835–41.
CAS
PubMed
Google Scholar
van der Aa LB, et al. Effect of a new synbiotic mixture on atopic dermatitis in infants: a randomized-controlled trial. Clin Exp Allergy. 2010;40(5):795–804.
PubMed
Google Scholar
de Kivit S, et al. Glycan recognition at the interface of the intestinal immune system: target for immune modulation via dietary components. Eur J Pharmacol. 2011;668(Suppl 1):S124–32.
PubMed
Google Scholar
Garin MI, et al. Galectin-1: a key effector of regulation mediated by CD4+CD25+ T cells. Blood. 2007;109(5):2058–65.
CAS
PubMed
Google Scholar
van der Leij J, et al. Strongly enhanced IL-10 production using stable galectin-1 homodimers. Mol Immunol. 2007;44(4):506–13.
PubMed
Google Scholar
Mitra SK, Hanson DA, Schlaepfer DD. Focal adhesion kinase: in command and control of cell motility. Nat Rev Mol Cell Biol. 2005;6(1):56–68.
CAS
PubMed
Google Scholar
Petit V, Thiery JP. Focal adhesions: structure and dynamics. Biol Cell. 2000;92(7):477–94.
CAS
PubMed
Google Scholar
Arnold JW, Roach J, Azcarate-Peril MA. Emerging technologies for gut microbiome research. Trends Microbiol. 2016;24(11):887–901.
CAS
PubMed
PubMed Central
Google Scholar
Tran L, Greenwood-Van Meerveld B. Age-associated remodeling of the intestinal epithelial barrier. J Gerontol A Biol Sci Med Sci. 2013;68(9):1045–56.
CAS
PubMed
PubMed Central
Google Scholar
Mitchell EL, et al. Reduced intestinal motility, mucosal barrier function, and inflammation in aged monkeys. J Nutr Health Aging. 2017;21(4):354–61.
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, et al. Effect of heat-inactivated Lactobacillus paracasei N1115 on microbiota and gut-brain axis related molecules. Biosci Microbiota Food Health. 2020;39(3):89–99.
PubMed
PubMed Central
Google Scholar
Gracz AD, et al. A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis. Nat Cell Biol. 2015;17(3):340–9.
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, et al. In vitro generation of colonic epithelium from primary cells guided by microstructures. Lab Chip. 2014;14(9):1622–31.
CAS
PubMed
PubMed Central
Google Scholar
Junick J, Blaut M. Quantification of human fecal bifidobacterium species by use of quantitative real-time PCR analysis targeting the groEL gene. Appl Environ Microbiol. 2012;78(8):2613–22.
CAS
PubMed
PubMed Central
Google Scholar
Matsuki T, et al. Quantitative PCR with 16S rRNA-gene-targeted species-specific primers for analysis of human intestinal bifidobacteria. Appl Environ Microbiol. 2004;70(1):167–73.
CAS
PubMed
PubMed Central
Google Scholar
Hermann-Bank, M.L., et al. The gut microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity. BMC Genomics. 2013;14:788.
Google Scholar
Kwon H-S, et al. Rapid identification of potentially probiotic Bifidobacterium species by multiplex PCR using species-specific primers based on the region extending from 16S rRNA through 23 S rRNA. FEMS Microbiol Lett. 2006;250(1):55–62.
Google Scholar
Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101–8.
CAS
PubMed
Google Scholar
Bolyen E, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–7.
CAS
PubMed
PubMed Central
Google Scholar
Vieira-Silva S, et al. Species-function relationships shape ecological properties of the human gut microbiome. Nat Microbiol. 2016;1(8):16088.
CAS
PubMed
Google Scholar
Magnusdottir S, et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol. 2017;35(1):81–9.
CAS
PubMed
Google Scholar
Paul De Vos, e., Bergey’s manual of systematic bacteriology: 2nd Dordrecht; Springer, [2009] ©2009.
Maruo T, et al. Adlercreutzia equolifaciens gen. nov., sp. nov., an equol-producing bacterium isolated from human faeces, and emended description of the genus Eggerthella. Int J Syst Evol Microbiol. 2008;58(Pt 5):1221–7.
CAS
PubMed
Google Scholar
Monteiro RA, et al. Use of lactose to induce expression of soluble NifA protein domains of Herbaspirillum seropedicae in Escherichia coli. Can J Microbiol. 2000;46(11):1087–90.
CAS
PubMed
Google Scholar
Brooke JS. Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clin Microbiol Rev. 2012;25(1):2–41.
CAS
PubMed
PubMed Central
Google Scholar
Kooken JM, Fox KF, Fox A. Characterization of Micrococcus strains isolated from indoor air. Mol Cell Probes. 2012;26(1):1–5.
CAS
PubMed
Google Scholar
Kuete E, et al. Brachybacterium timonense sp. nov., a new bacterium isolated from human sputum. New Microbes New Infect. 2019;31:100568.
CAS
PubMed
PubMed Central
Google Scholar
Duskova D, Marounek M. Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rumen bacterium Lachnospira multiparus. Lett Appl Microbiol. 2001;33(2):159–63.
CAS
PubMed
Google Scholar
Kasperowicz A, et al. Sucrose phosphorylase of the rumen bacterium Pseudobutyrivibrio ruminis strain A. J Appl Microbiol. 2009;107(3):812–20.
CAS
PubMed
Google Scholar
Petzel JP, Hartman PA. Aromatic amino acid biosynthesis and carbohydrate catabolism in strictly anaerobic mollicutes (Anaeroplasma spp.). Systematic and Applied Microbiology. 1990;13(3):240–7.
CAS
Google Scholar
Wallace RJ, et al. Eubacterium pyruvativorans sp. nov., a novel non-saccharolytic anaerobe from the rumen that ferments pyruvate and amino acids, forms caproate and utilizes acetate and propionate. Int J Syst Evol Microbiol. 2003;53(Pt 4):965–70.
CAS
PubMed
Google Scholar
Tarlera S, et al. Caloramator proteoclasticus sp. nov., a new moderately thermophilic anaerobic proteolytic bacterium. Int J Syst Bacteriol. 1997;47(3):651–6.
CAS
PubMed
Google Scholar
Collins MD, et al. Phenotypic and phylogenetic characterization of some Globicatella-like organisms from human sources: description of Facklamia hominis gen. nov., sp. nov. Int J Syst Bacteriol. 1997;47(3):880–2.
CAS
PubMed
Google Scholar
Heyndrickx M, et al. Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998. Int J Syst Bacteriol. 1999;49(Pt 3):1083–90.
CAS
PubMed
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
CAS
PubMed
PubMed Central
Google Scholar
Abubucker S, et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012;8(6):e1002358.
CAS
PubMed
PubMed Central
Google Scholar
Okazaki R, et al. The crucial role of Erk2 in demyelinating inflammation in the central nervous system. J Neuroinflamm. 2016;13(1):235.
Google Scholar
Yang Y, et al. Chemoprevention of dietary digitoflavone on colitis-associated colon tumorigenesis through inducing Nrf2 signaling pathway and inhibition of inflammation. Mol Cancer. 2014;13(1):48.
CAS
PubMed
PubMed Central
Google Scholar
Shigemura H. Up-regulation of MUC2 mucin expression by serum amyloid A3 protein in mouse. J Vet Med Sci. 2014;76(7):985–91. https://doi.org/10.1292/jvms.14-0007. Epub 2014 Apr 1.
Wlodarska M, et al. Antibiotic treatment alters the colonic mucus layer and predisposes the host to exacerbated Citrobacter rodentium-induced colitis. Infect Immun. 2011;79(4):1536–45.
CAS
PubMed
PubMed Central
Google Scholar
Morampudi V, et al. The goblet cell-derived mediator RELM-beta drives spontaneous colitis in Muc2-deficient mice by promoting commensal microbial dysbiosis. Mucosal Immunol. 2016;9(5):1218–33.
CAS
PubMed
Google Scholar
Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
CAS
PubMed
Google Scholar
Patro R, et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417–9.
CAS
PubMed
PubMed Central
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
PubMed
PubMed Central
Google Scholar
Mandal S, et al. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015;26:27663.
PubMed
Google Scholar
Parks DH, et al. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30(21):3123–4.
CAS
PubMed
PubMed Central
Google Scholar