Karl JP, Hatch AM, Arcidiacono SM, Pearce SC, Pantoja-Feliciano IG, Doherty LA, Soares JW. Effects of Psychological, Environmental and Physical Stressors on the Gut Microbiota. Front Microbiol. 2013;2018:9.

Google Scholar 

Griffin NW, Ahern PP, Cheng J, Heath AC, Ilkayeva O, Newgard CB, Fontana L, Gordon JI. Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions. Cell Host Microbe. 2017;21(1):84–96.

Article  CAS  Google Scholar 

Xiao S, Fei N, Pang X, Shen J, Wang L, Zhang B, Zhang M, Zhang X, Zhang C, Li M, et al. A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome. FEMS Microbiol Ecol. 2014;87(2):357–67.

Article  CAS  Google Scholar 

Chen X, Li HY, Hu XM, Zhang Y, Zhang SY. Current understanding of gut microbiota alterations and related therapeutic intervention strategies in heart failure. Chin Med J (Engl). 2019;132(15):1843–55.

Article  CAS  Google Scholar 

Haak BW, Prescott HC, Wiersinga WJ. Therapeutic Potential of the Gut Microbiota in the Prevention and Treatment of Sepsis. Front Immunol. 2018;9:2042.

Article  Google Scholar 

Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, Kim AD, Shmagel AK, Syed AN, Personalized Microbiome Class S, et al. Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans. Cell Host Microbe. 2019;25(6):789–802 e785.

Article  CAS  Google Scholar 

Karl JP, Armstrong NJ, McClung HL, Player RA, Rood JC, Racicot K, Soares JW, Montain SJ. A diet of US military food rations alters gut microbiota composition and does not increase intestinal permeability. J Nutr Biochem. 2019;72:108217.

Article  CAS  Google Scholar 

Pantoja-Feliciano IG, Soares JW, Doherty LA, Karl JP, McClung HL, Armstrong NJ, Branck TA, Arcidiacono S. Acute stressor alters inter-species microbial competition for resistant starch-supplemented medium. Gut Microbes. 2019;10(4):439–46.

Article  CAS  Google Scholar 

Bastiaanssen TFS, Gururajan A, van de Wouw M, Moloney GM, Ritz NL, Long-Smith CM, Wiley NC, Murphy AB, Lyte JM, Fouhy F, et al. Volatility as a Concept to Understand the Impact of Stress on the Microbiome. Psychoneuroendocrinology. 2021;124: 105047.

Article  CAS  Google Scholar 

Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 2015;9(4):968–79.

Article  CAS  Google Scholar 

Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, et al. Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018;15(11):962–8.

Article  CAS  Google Scholar 

Martinez I, Kim J, Duffy PR, Schlegel VL, Walter J. 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.

Article  CAS  Google Scholar 

Lyte M, Chapel A, Lyte JM, Ai Y, Proctor A, Jane JL, Phillips GJ. Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior. PLoS ONE. 2016;11(1): e0146406.

Article  Google Scholar 

Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Dore J, Henrissat B, Remaud-Simeon M, Monsan P, Potocki-Veronese G. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS ONE. 2013;8(9): e72766.

Article  CAS  Google Scholar 

Taras D, Simmering R, Collins MD, Lawson PA, Blaut M. Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen nov comb nov and description of Dorea longicatena sp nov isolated from human faeces. Int J Syst Evol Microbiol. 2002;52(Pt 2):423–8.

Article  Google Scholar 

Herrmann E, Young W, Reichert-Grimm V, Weis S, Riedel CU, Rosendale D, Stoklosinski H, Hunt M, Egert M. In Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using RNA-Based Stable Isotope Probing-A Proof-of-Principle Study. Nutrients. 2018;10(2):179-96.

Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, et al. Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Sci Rep. 2016;6:28484.

Article  CAS  Google Scholar 

Power SE, O’Toole PW, Stanton C, Ross RP, Fitzgerald GF. Intestinal microbiota, diet and health. Br J Nutr. 2014;111(3):387–402.

Article  CAS  Google Scholar 

De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, et al. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut. 2016;65(11):1812–21.

Article  Google Scholar 

Bang SJ, Kim G, Lim MY, Song EJ, Jung DH, Kum JS, Nam YD, Park CS, Seo DH. The influence of in vitro pectin fermentation on the human fecal microbiome. AMB Express. 2018;8(1):98.

Article  Google Scholar 

Danneskiold-Samsoe NB. Dias de Freitas Queiroz Barros H, Santos R, Bicas JL, Cazarin CBB, Madsen L, Kristiansen K, Pastore GM, Brix S, Marostica Junior MR: Interplay between food and gut microbiota in health and disease. Food Res Int. 2019;115:23–31.

Article  Google Scholar 

Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science. 2001;292(5519):1115–8.

Article  CAS  Google Scholar 

Wexler HM. Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev. 2007;20(4):593–621.

Article  CAS  Google Scholar 

Purcell RV. "Bacteroides fragilis." Colorectal Neoplasia and the Colorectal Microbiome Dysplasia, Probiotics, and Fusobacteria, edited by Floch, MH. Academic Press; 2020. p. 57-77.

Rios-Covian D, Sanchez B, Salazar N, Martinez N, Redruello B, Gueimonde M, de Los Reyes-Gavilan CG. Different metabolic features of Bacteroides fragilis growing in the presence of glucose and exopolysaccharides of bifidobacteria. Front Microbiol. 2015;6:825.

Article  Google Scholar 

Ze XL, Duncan SH, Louis P, Flint HJ. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 2012;6(8):1535–43.

Article  CAS  Google Scholar 

Apajalahti JH, Kettunen A, Nurminen PH, Jatila H, Holben WE. Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces. Appl Environ Microbiol. 2003;69(9):5731–5.

Article  CAS  Google Scholar 

Belenguer A, Duncan SH, Calder AG, Holtrop G, Louis P, Lobley GE, Flint HJ. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol. 2006;72(5):3593–9.

Article  CAS  Google Scholar 

Png CW, Linden SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, McGuckin MA, Florin TH. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol. 2010;105(11):2420–8.

Article  CAS  Google Scholar 

Rajilic-Stojanovic M, Shanahan F, Guarner F, de Vos WM. Phylogenetic analysis of dysbiosis in ulcerative colitis during remission. Inflamm Bowel Dis. 2013;19(3):481–8.

Article  Google Scholar 

Keenan MJ, Janes M, Robert J, Martin RJ, Raggio AM, McCutcheon KL, Pelkman C, Tulley R, Goita M, Durham HA, et al. Resistant starch from high amylose maize (HAM-RS2) reduces body fat and increases gut bacteria in ovariectomized (OVX) rats. Obesity (Silver Spring). 2013;21(5):981–4.

Article  CAS  Google Scholar 

Maier TV, Lucio M, Lee LH, VerBerkmoes NC, Brislawn CJ, Bernhardt J, Lamendella R, McDermott JE, Bergeron N, Heinzmann SS, et al. Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. mBio. 2017;8(5):e01343-17.

Kabiri L, Alum A, Rock C, McLain JE, Abbaszadegan M. Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers. Can J Microbiol. 2013;59(12):771–7.

Article  CAS  Google Scholar 

Kmezik C, Krska D, Mazurkewich S, Larsbrink J. Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii. Sci Rep. 2021;11(1):17662.

Article  CAS  Google Scholar 

Wang Y, Mortimer EK, Katundu KGH, Kalanga N, Leong LEX, Gopalsamy GL, Christophersen CT, Richard AC, Shivasami A, Abell GCJ, et al. The Capacity of the Fecal Microbiota From Malawian Infants to Ferment Resistant Starch. Front Microbiol. 2019;10:1459.

Article  Google Scholar 

Warren FJ, Fukuma NM, Mikkelsen D, Flanagan BM, Williams BA, Lisle AT, P OC, Morrison M, Gidley MJ. Food Starch Structure Impacts Gut Microbiome Composition. mSphere. 2018;3(3):e00086-18.

Cho GS, Ritzmann F, Eckstein M, Huch M, Briviba K, Behsnilian D, Neve H, Franz CM. Quantification of Slackia and Eggerthella spp in Human Feces and Adhesion of Representatives Strains to Caco-2 Cells. Front Microbiol. 2016;7:658.

Article  Google Scholar 

Oliphant K, Allen-Vercoe E. Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. Microbiome. 2019;7(1):91.

Article  Google Scholar 

Pinto E, Anselmo M, Calha M, Bottrill A, Duarte I, Andrew PW, Faleiro ML. The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins. Microbiology. 2017;163(2):161–74.

Article  CAS  Google Scholar 

Salyers AA, West SE, Vercellotti JR, Wilkins TD. Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon. Appl Environ Microbiol. 1977;34(5):529–33.

Article  CAS  Google Scholar 

Low KE, Xing X, Moote PE, Inglis GD, Venketachalam S, Hahn MG, King ML, Tetard-Jones CY, Jones DR, Willats WGT, et al. Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides. Microorganisms. 2020;8(12):1888-913.

Lou YC, Olm MR, Diamond S, Crits-Christoph A, Firek BA, Baker R, Morowitz MJ, Banfield JF. Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition. Cell Rep Med. 2021;2(9): 100393.

Article  CAS  Google Scholar 

McInnes P. Manual of Procedures for Human Microbiome Project Core Microbiome Sampling-Protocol A, HMP Protocol # 07–001. National Institute of Health. 2010; Version 12.0, Accession number: phd003190.2.

Macfarlane GT, Macfarlane S, Gibson GR. Validation of a Three-Stage Compound Continuous Culture System for Investigating the Effect of Retention Time on the Ecology and Metabolism of Bacteria in the Human Colon. Microb Ecol. 1998;35(2):180–7.

Article  CAS  Google Scholar 

Aguirre M, Ramiro-Garcia J, Koenen ME, Venema K. To pool or not to pool? Impact of the use of individual and pooled fecal samples for in vitro fermentation studies. J Microbiol Methods. 2014;107:1–7.

Article  CAS  Google Scholar 

Apprill AMS, Parsons R, Weber L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat Microb Ecol. 2015;75:129–37.

Article  Google Scholar 

Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. En