Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait

References

• Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635–27. doi:10.1126/science.1110591.
   PubMed Web of Science ®Google Scholar
• Coyte KZ, Rakoff-Nahoum S. Understanding competition and cooperation within the mammalian gut microbiome. Curr Biol. 2019;29(11):R538–R44. doi:10.1016/j.cub.2019.04.017.
   PubMed Web of Science ®Google Scholar
• Cani PD. Human gut microbiome: hopes, threats and promises. Gut. 2018;67(9):1716–1725. doi:10.1136/gutjnl-2018-316723.
   PubMed Web of Science ®Google Scholar
• Lynch SV, Pedersen O, Phimister EG. The human intestinal microbiome in health and disease. N Engl J Med. 2016;375(24):2369–2379. doi:10.1056/NEJMra1600266.
   PubMed Web of Science ®Google Scholar
• Clemente JC, Ursell LK, Parfrey LW, Knight R. The impact of the gut microbiota on human health: an integrative view. Cell. 2012;148(6):1258–1270. doi:10.1016/j.cell.2012.01.035.
   PubMed Web of Science ®Google Scholar
• O’Hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006;7(7):688–693. doi:10.1038/sj.embor.7400731.
   PubMed Web of Science ®Google Scholar
• Crowley EK, Long-Smith CM, Murphy A, Patterson E, Murphy K, O’Gorman DM, Stanton C, Nolan Y. Dietary supplementation with a magnesium-rich marine mineral blend enhances the diversity of gastrointestinal microbiota. Mar Drugs. 2018;16(6):216. doi:10.3390/md16060216.
   PubMed Web of Science ®Google Scholar
• Bielik V, Kolisek M. Bioaccessibility and bioavailability of minerals in relation to a healthy gut microbiome. Int J Mol Sci. 2021;22(13):6803. doi:10.3390/ijms22136803.
   PubMed Web of Science ®Google Scholar
• Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, Tuohy K. Gut microbiota functions: metabolism of nutrients and other food components. Eur J Nutr. 2018;57(1):1–24. doi:10.1007/s00394-017-1445-8.
   PubMed Web of Science ®Google Scholar
• de Vos WM, de Vos WM. Microbial biofilms and the human intestinal microbiome. NPJ Biofilms Microbiomes. 2015;1(1):15005. doi:10.1038/npjbiofilms.2015.5.
   PubMedGoogle Scholar
• Rossi M, Amaretti A, Raimondi S. Folate production by probiotic bacteria. Nutrients. 2011;3(1):118–134. doi:10.3390/nu3010118.
   PubMed Web of Science ®Google Scholar
• Solopova A, Bottacini F, Venturi Degli Esposti E, Amaretti A, Raimondi S, Rossi M, van Sinderen D. Riboflavin biosynthesis and overproduction by a derivative of the human gut commensal Bifidobacterium longum subsp. infantis ATCC 15697. Front Microbiol. 2020;11:573335. doi:10.3389/fmicb.2020.573335.
   PubMed Web of Science ®Google Scholar
• Leatham MP, Banerjee S, Autieri SM, Mercado-Lubo R, Conway T, Cohen PS. Precolonized human commensal Escherichia coli strains serve as a barrier to E. coli O157: H7 growth in the streptomycin-treated mouse intestine. Infect Immun. 2009;77(7):2876–2886. doi:10.1128/IAI.00059-09.
   PubMed Web of Science ®Google Scholar
• Durso LM, Smith D, Hutkins RW. Measurements of fitness and competition in commensal Escherichia coli and E. coli O157: H7 strains. Appl Environ Microbiol. 2004;70(11):6466–6472. doi:10.1128/AEM.70.11.6466-6472.2004.
   PubMed Web of Science ®Google Scholar
• Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev. 2017;81(4). doi:10.1128/MMBR.00036-17.
   PubMed Web of Science ®Google Scholar
• Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122(1):107–118. doi:10.1016/j.cell.2005.05.007.
   PubMed Web of Science ®Google Scholar
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–563. doi:10.1038/nature12820.
   PubMed Web of Science ®Google Scholar
• Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Sci. 2016;352(6285):539–544. doi:10.1126/science.aad9378.
   PubMed Web of Science ®Google Scholar
• Al Nabhani Z, Eberl G. Imprinting of the immune system by the microbiota early in life. Mucosal Immunol. 2020;13(2):183–189. doi:10.1038/s41385-020-0257-y.
   PubMed Web of Science ®Google Scholar
• Ganal-Vonarburg SC, Hornef MW, Macpherson AJ. Microbial-host molecular exchange and its functional consequences in early mammalian life. Science. 2020;368(6491):604–607. doi:10.1126/science.aba0478.
   PubMed Web of Science ®Google Scholar
• Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444(7122):1022–1023. doi:10.1038/4441022a.
   PubMed Web of Science ®Google Scholar
• Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533. doi:10.1371/journal.pbio.1002533.
   PubMed Web of Science ®Google Scholar
• Browne HP, Neville BA, Forster SC, Lawley TD. Transmission of the gut microbiota: spreading of health. Nat Rev Microbiol. 2017;15(9):531–543. doi:10.1038/nrmicro.2017.50.
   PubMed Web of Science ®Google Scholar
• Louis P, Hold GL, Flint HJ. The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol. 2014;12(10):661–672. doi:10.1038/nrmicro3344.
   PubMed Web of Science ®Google Scholar
• Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AH, FitzGerald MG, Fulton RS. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–214.
   PubMed Web of Science ®Google Scholar
• Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, et al. Enterotypes of the human gut microbiome. Nature. 2011;473(7346):174–180. doi:10.1038/nature09944.
   PubMed Web of Science ®Google Scholar
• Iacob S, Iacob DG. Infectious threats, the intestinal barrier, and its trojan horse: dysbiosis. Front Microbiol. 2019;10:1676. doi:10.3389/fmicb.2019.01676.
   PubMed Web of Science ®Google Scholar
• Yassour M, Vatanen T, Siljander H, Hamalainen AM, Harkonen T, Ryhanen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med. 2016;8(343):343ra81. doi:10.1126/scitranslmed.aad0917.
   PubMed Web of Science ®Google Scholar
• Pereira FC, Berry D. Microbial nutrient niches in the gut. Environ Microbiol. 2017;19(4):1366–1378. doi:10.1111/1462-2920.13659.
   PubMed Web of Science ®Google Scholar
• Messer JS, Liechty ER, Vogel OA, Chang EB. Evolutionary and ecological forces that shape the bacterial communities of the human gut. Mucosal Immunol. 2017;10(3):567–579. doi:10.1038/mi.2016.138.
   PubMed Web of Science ®Google Scholar
• Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut microbiota in health and disease. Physiol Rev. 2010;90(3):859–904. doi:10.1152/physrev.00045.2009.
   PubMed Web of Science ®Google Scholar
• Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555(7695):210–215. doi:10.1038/nature25973.
   PubMed Web of Science ®Google Scholar
• Ghosh TS, Rampelli S, Jeffery IB, Santoro A, Neto M, Capri M, Giampieri E, Jennings A, Candela M, Turroni S, et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut. 2020;69(7):gutjnl-2019–319654. doi:10.1136/gutjnl-2019-319654.
   Web of Science ®Google Scholar
• Maldonado-Gomez MX, Martinez I, Bottacini F, O’Callaghan A, Ventura M, van Sinderen D, Hillmann B, Vangay P, Knights D, Hutkins R, et al. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host & Microbe. 2016;20(4):515–526. doi:10.1016/j.chom.2016.09.001.
   PubMed Web of Science ®Google Scholar
• Marchesi JR, Adams DH, Fava F, Hermes GD, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, et al. The gut microbiota and host health: a new clinical frontier. Gut. 2016;65(2):330–339. doi:10.1136/gutjnl-2015-309990.
   PubMed Web of Science ®Google Scholar
• Glover JS, Ticer TD, Engevik MA. Characterizing the mucin-degrading capacity of the human gut microbiota. Sci Rep. 2022;12(1):8456. doi:10.1038/s41598-022-11819-z.
   PubMed Web of Science ®Google Scholar
• Townsend GE 2nd, Han W, Schwalm ND 3rd, Raghavan V, Barry NA, Goodman AL, Groisman EA. Dietary sugar silences a colonization factor in a mammalian gut symbiont. Proc Natl Acad Sci USA. 2019;116(1):233–238. doi:10.1073/pnas.1813780115.
   PubMed Web of Science ®Google Scholar
• Fu X, Liu Z, Zhu C, Mou H, Kong Q. Nondigestible carbohydrates, butyrate, and butyrate-producing bacteria. Crit Rev Food Sci Nutr. 2019;59(sup1):S130–S52. doi:10.1080/10408398.2018.1542587.
   PubMed Web of Science ®Google Scholar
• Liu H, Wang J, He T, Becker S, Zhang G, Li D, Ma X. Butyrate: a double-edged sword for health? Adv Nutr. 2018;9(1):21–29. doi:10.1093/advances/nmx009.
   PubMed Web of Science ®Google Scholar
• McCarville JL, Chen GY, Cuevas VD, Troha K, Ayres JS. Microbiota metabolites in health and disease. Annu Rev Immunol. 2020;38(1):147–170. doi:10.1146/annurev-immunol-071219-125715.
   PubMedGoogle Scholar
• Miranda RL, Conway T, Leatham MP, Chang DE, Norris WE, Allen JH, Stevenson SJ, Laux DC, Cohen PS. Glycolytic and gluconeogenic growth of Escherichia coli O157: H7 (EDL933) and E. coli K-12 (MG1655) in the mouse intestine. Infect Immun. 2004;72(3):1666–1676. doi:10.1128/IAI.72.3.1666-1676.2004.
   PubMed Web of Science ®Google Scholar
• Morin M, Ropers D, Cinquemani E, Portais JC, Enjalbert B, Cocaign-Bousquet M, Romeo T, Greenberg EP. The CSR system regulates Escherichia coli fitness by controlling glycogen accumulation and energy levels. mBio. 2017;8(5). doi:10.1128/mBio.01628-17.
   PubMed Web of Science ®Google Scholar
• Jones SA, Jorgensen M, Chowdhury FZ, Rodgers R, Hartline J, Leatham MP, Struve C, Krogfelt KA, Cohen PS, Conway T, et al. Glycogen and maltose utilization by Escherichia coli O157: H7 in the mouse intestine. Infect Immun. 2008;76(6):2531–2540. doi:10.1128/IAI.00096-08.
   PubMed Web of Science ®Google Scholar
• Fabich AJ, Jones SA, Chowdhury FZ, Cernosek A, Anderson A, Smalley D, McHargue JW, Hightower GA, Smith JT, Autieri SM, et al. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect Immun. 2008;76(3):1143–1152. doi:10.1128/IAI.01386-07.
   PubMed Web of Science ®Google Scholar
• Kamada N, Chen GY, Inohara N, Nunez G. Control of pathogens and pathobionts by the gut microbiota. Nat Immunol. 2013;14(7):685–690. doi:10.1038/ni.2608.
   PubMed Web of Science ®Google Scholar
• Ventura M, O’Flaherty S, Claesson MJ, Turroni F, Klaenhammer TR, van Sinderen D, O’Toole PW. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat Rev Microbiol. 2009;7(1):61–71. doi:10.1038/nrmicro2047.
   PubMed Web of Science ®Google Scholar
• Seibold G, Dempf S, Schreiner J, Eikmanns BJ. Glycogen formation in Corynebacterium glutamicum and role of ADP-glucose pyrophosphorylase. Microbiology. 2007;153(Pt 4):1275–1285. doi:10.1099/mic.0.2006/003368-0.
   PubMedGoogle Scholar
• Cifuente JO, Comino N, Trastoy B, D’Angelo C, Guerin ME. Structural basis of glycogen metabolism in bacteria. Biochem J. 2019;476(14):2059–2092. doi:10.1042/BCJ20170558.
   PubMedGoogle Scholar
• Ayres JS. Cooperative microbial tolerance behaviors in host-microbiota mutualism. Cell. 2016;165(6):1323–1331. doi:10.1016/j.cell.2016.05.049.
   PubMed Web of Science ®Google Scholar
• Gonzalez-Rodriguez I, Ruiz L, Gueimonde M, Margolles A, Sanchez B. Factors involved in the colonization and survival of bifidobacteria in the gastrointestinal tract. FEMS Microbiol Lett. 2013;340(1):1–10. doi:10.1111/1574-6968.12056.
   PubMed Web of Science ®Google Scholar
• Fallingborg J. Intraluminal pH of the human gastrointestinal tract. Dan Med Bull. 1999;46:183–196.
   PubMed Web of Science ®Google Scholar
• Koziolek M, Grimm M, Becker D, Iordanov V, Zou H, Shimizu J, Wanke C, Garbacz G, Weitschies W. Investigation of pH and temperature profiles in the GI tract of fasted human subjects using the intellicap® system. J Pharm Sci. 2015;104(9):2855–2863. doi:10.1002/jps.24274.
   PubMed Web of Science ®Google Scholar
• Cheng S, Zhu L, Faden HS. Interactions of bile acids and the gut microbiota: learning from the differences in Clostridium difficile infection between children and adults. Physiol Genomics. 2019;51(6):218–223. doi:10.1152/physiolgenomics.00034.2019.
   PubMed Web of Science ®Google Scholar
• Drasar BS, Hill MJ, Shiner M. The deconjugation of bile salts by human intestinal bacteria. Lancet. 1966;1(7449):1237–1238. doi:10.1016/S0140-6736(66)90242-X.
   PubMed Web of Science ®Google Scholar
• Ferrari A, Pacini N, Canzi E. A note on bile acids transformations by strains of Bifidobacterium. J Appl Bacteriol. 1980;49(2):193–197. doi:10.1111/j.1365-2672.1980.tb05117.x.
   PubMedGoogle Scholar
• Gilliland SE, Speck ML. Deconjugation of bile acids by intestinal lactobacilli. Appl Environ Microbiol. 1977;33(1):15–18. doi:10.1128/aem.33.1.15-18.1977.
   PubMed Web of Science ®Google Scholar
• Moser SA, Savage DC. Bile salt hydrolase activity and resistance to toxicity of conjugated bile salts are unrelated properties in lactobacilli. Appl Environ Microbiol. 2001;67(8):3476–3480. doi:10.1128/AEM.67.8.3476-3480.2001.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Fanning S, Hall LJ, Cronin M, Zomer A, MacSharry J, Goulding D, O’Connell Motherway M, Shanahan F, Nally K, Dougan G, et al. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc Natl Acad Sci U S A. 2012;109(6):2108–2113. doi:10.1073/pnas.1115621109.
   PubMed Web of Science ®Google Scholar
• Ruiz L, Zomer A, O’Connell-Motherway M, van Sinderen D, Margolles A. Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics. Appl Environ Microbiol. 2012;78(4):1123–1131. doi:10.1128/AEM.06060-11.
   PubMed Web of Science ®Google Scholar
• Ruas-Madiedo P, Gueimonde M, Arigoni F, de Los Reyes-Gavilan CG, Margolles A, de Los Reyes-Gavilán CG. Bile affects the synthesis of exopolysaccharides by Bifidobacterium animalis. Appl Environ Microbiol. 2009;75(4):1204–1207. doi:10.1128/AEM.00908-08.
   PubMed Web of Science ®Google Scholar
• Du D, Wang Z, James NR, Voss JE, Klimont E, Ohene-Agyei T, Venter H, Chiu W, Luisi BF. Structure of the AcrAB–TolC multidrug efflux pump. Nature. 2014;509(7501):512–515. doi:10.1038/nature13205.
   PubMed Web of Science ®Google Scholar
• Laparra JM, Sanz Y. Comparison of in vitro models to study bacterial adhesion to the intestinal epithelium. Lett Appl Microbiol. 2009;49(6):695–701. doi:10.1111/j.1472-765X.2009.02729.x.
   PubMed Web of Science ®Google Scholar
• Tuomola E, Crittenden R, Playne M, Isolauri E, Salminen S. Quality assurance criteria for probiotic bacteria. Am J Clin Nutr. 2001;73(2 Suppl):393S–398S. doi:10.1093/ajcn/73.2.393s.
   PubMed Web of Science ®Google Scholar
• Saffarian A, Mulet C, Regnault B, Amiot A, Tran-Van-Nhieu J, Ravel J, Sobhani I, Sansonetti PJ, Pédron T, et al. Crypt- and mucosa-associated core microbiotas in humans and their alteration in colon cancer patients and mucosa-associated core microbiotas in humans and their alteration in colon cancer patients. mBio. 2019;10(4). doi:10.1128/mBio.01315-19.
   PubMed Web of Science ®Google Scholar
• Pedron T, Nigro G, Sansonetti PJ. From homeostasis to pathology: decrypting microbe–host symbiotic signals in the intestinal crypt. Philos Trans R Soc Lond B Biol Sci. 2016;371(1707):20150500. doi:10.1098/rstb.2015.0500.
   PubMed Web of Science ®Google Scholar
• Capurso L, Delle Fave G, Morelli L. Probiotics, prebiotics, and new foods. J Clin Gastroenterol. 2008;42(Suppl 3 Pt 2):S155. doi:10.1097/MCG.0b013e31817e55b2.
   PubMedGoogle Scholar
• Castro-Bravo N, Sánchez B, Margolles A, Ruas-Madiedo P. Chapter 10 - biological activities and applications of bifidobacterial exopolysaccharides: from the bacteria and host perspective. In: Mattarelli P, Biavati B, Holzapfel W Wood B, editors. The bifidobacteria and related. Organisms:Academic Press; 2018. pp. 177–193. doi:10.1016/B978-0-12-805060-6.00010-7.
   Google Scholar
• Lee IC, Caggianiello G, van S II, Taverne N, Meijerink M, PA B, Spano G, Kleerebezem M. Strain-specific features of extracellular polysaccharides and their impact on lactobacillus plantarum-host interactions. Appl Environ Microbiol. 2016;82(13):3959–3970. doi:10.1128/AEM.00306-16.
   PubMed Web of Science ®Google Scholar
• Dertli E, Mayer MJ, Narbad A. Impact of the exopolysaccharide layer on biofilms, adhesion and resistance to stress in Lactobacillus johnsonii FI9785. BMC Microbiol. 2015;15(1):8. doi:10.1186/s12866-015-0347-2.
   PubMedGoogle Scholar
• Denou E, Pridmore RD, Berger B, Panoff JM, Arigoni F, Brussow H. Identification of genes associated with the long-gut-persistence phenotype of the probiotic Lactobacillus johnsonii strain NCC533 using a combination of genomics and transcriptome analysis. J Bacteriol. 2008;190(9):3161–3168. doi:10.1128/JB.01637-07.
   PubMed Web of Science ®Google Scholar
• Tahoun A, Masutani H, El-Sharkawy H, Gillespie T, Honda RP, Kuwata K, Inagaki M, Yabe T, Nomura I, Suzuki T, et al. Capsular polysaccharide inhibits adhesion of Bifidobacterium longum 105-A to enterocyte-like Caco-2 cells and phagocytosis by macrophages. Gut Pathog. 2017;9(1):27. doi:10.1186/s13099-017-0177-x.
   PubMedGoogle Scholar
• Lebeer S, Verhoeven TL, Francius G, Schoofs G, Lambrichts I, Dufrene Y, Vanderleyden J, De Keersmaecker SCJ. Identification of a gene cluster for the biosynthesis of a long, galactose-rich exopolysaccharide in lactobacillus rhamnosus gg and functional analysis of the priming glycosyltransferase. Appl Environ Microbiol. 2009;75(11):3554–3563. doi:10.1128/AEM.02919-08.
   PubMed Web of Science ®Google Scholar
• Craig L, Li J. Type IV pili: paradoxes in form and function. Curr Opin Struct Biol. 2008;18(2):267–277. doi:10.1016/j.sbi.2007.12.009.
   PubMed Web of Science ®Google Scholar
• Hendrickx AP, Budzik JM, Oh SY, Schneewind O. Architects at the bacterial surface - sortases and the assembly of pili with isopeptide bonds. Nat Rev Microbiol. 2011;9(3):166–176. doi:10.1038/nrmicro2520.
   PubMed Web of Science ®Google Scholar
• Reunanen J, von Ossowski I, Hendrickx AP, Palva A, de Vos WM. Characterization of the SpaCBA pilus fibers in the probiotic Lactobacillus rhamnosus GG. Appl Environ Microbiol. 2012;78(7):2337–2344. doi:10.1128/AEM.07047-11.
   PubMed Web of Science ®Google Scholar
• Turroni F, Foroni E, Serafini F, Viappiani A, Montanini B, Bottacini F, Ferrarini A, Bacchini PL, Rota C, Delledonne M, et al. Ability of Bifidobacterium breve to grow on different types of milk: exploring the metabolism of milk through genome analysis. Appl Environ Microbiol. 2011;77(20):7408–7417. doi:10.1128/AEM.05336-11.
   PubMed Web of Science ®Google Scholar
• Oxaran V, Ledue-Clier F, Dieye Y, Herry JM, Pechoux C, Meylheuc T, Briandet R, Juillard V, Piard JC. Pilus biogenesis in Lactococcus lactis: molecular characterization and role in aggregation and biofilm formation. PLoS One. 2012;7(12):e50989. doi:10.1371/journal.pone.0050989.
   PubMed Web of Science ®Google Scholar
• Yu X, Jaatinen A, Rintahaka J, Hynonen U, Lyytinen O, Kant R, Åvall-Jääskeläinen S, von Ossowski I, Palva A. Human gut-commensalic lactobacillus ruminis ATCC 25644 displays sortase-assembled surface piliation: phenotypic characterization of its fimbrial operon through in silico predictive analysis and recombinant expression in Lactococcus lactis. PLoS One. 2015;10(12):e0145718. doi:10.1371/journal.pone.0145718.
   PubMed Web of Science ®Google Scholar
• Proft T, Baker EN. Pili in gram-negative and gram-positive bacteria - structure, assembly and their role in disease. Cell Mol Life Sci. 2009;66(4):613–635. doi:10.1007/s00018-008-8477-4.
   PubMed Web of Science ®Google Scholar
• O’Connell Motherway M, Houston A, O’Callaghan G, Reunanen J, O’Brien F, O’Driscoll T, Casey PG, de Vos WM, van Sinderen D, Shanahan F. A Bifidobacterial pilus-associated protein promotes colonic epithelial proliferation. Mol Microbiol. 2019;111(1):287–301. doi:10.1111/mmi.14155.
   PubMed Web of Science ®Google Scholar
• O’Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Moreno Munoz JA, et al. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci U S A. 2011;108(27):11217–11222. doi:10.1073/pnas.1105380108.
   PubMed Web of Science ®Google Scholar
• Zmasek CM, Godzik A. Phylogenomic analysis of glycogen branching and debranching enzymatic duo. BMC Evol Biol. 2014;14(1):183. doi:10.1186/s12862-014-0183-2.
   PubMedGoogle Scholar
• Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3(4):289–306. doi:10.4161/gmic.19897.
   PubMed Web of Science ®Google Scholar
• Porter NT, Martens EC. The critical roles of polysaccharides in gut microbial ecology and physiology. Annu Rev Microbiol. 2017;71(1):349–369. doi:10.1146/annurev-micro-102215-095316.
   PubMedGoogle Scholar
• Goh YJ, Klaenhammer TR. Insights into glycogen metabolism in Lactobacillus acidophilus: impact on carbohydrate metabolism, stress tolerance and gut retention. Microb Cell Fact. 2014;13(1):94. doi:10.1186/s12934-014-0094-3.
   PubMedGoogle Scholar
• Park K-H. Roles of enzymes in glycogen metabolism and degradation in Escherichia coli. J Appl Glycosci. 2015;62(2):37–45. doi:10.5458/jag.jag.JAG-2015_005.
   Google Scholar
• Wilson WA, Roach PJ, Montero M, Baroja-Fernandez E, Munoz FJ, Eydallin G, Viale AM, Pozueta-Romero J. Regulation of glycogen metabolism in yeast and bacteria. FEMS Microbiol Rev. 2010;34(6):952–985. doi:10.1111/j.1574-6976.2010.00220.x.
   PubMed Web of Science ®Google Scholar
• Cedergren B, Holme T. On the glycogen in Escherichia coli B; electron microscopy of ultrathin sections of cells. J Ultrastruct Res. 1959;3(1):70–73. doi:10.1016/S0022-5320(59)80016-2.
   PubMedGoogle Scholar
• Strydom L, Jewell J, Meier MA, George GM, Pfister B, Zeeman S, Kossmann J, Lloyd JR. Analysis of genes involved in glycogen degradation in Escherichia coli. FEMS Microbiol Lett. 2017;364(3):fnx016. doi:10.1093/femsle/fnx016.
   Web of Science ®Google Scholar
• Levine S, Stevenson HJ, Tabor EC, Bordner RH, Chambers LA. Glycogen of enteric bacteria. J Bacteriol. 1953;66(6):664–670. doi:10.1128/jb.66.6.664-670.1953.
   PubMed Web of Science ®Google Scholar
• Strange RE, Dark FA, Ness AG. The survival of stationary phase aerobacter aerogenes stored in aqueous suspension. J Gen Microbiol. 1961;25(1):61–76. doi:10.1099/00221287-25-1-61.
   Google Scholar
• Wilkinson JF. Carbon and energy storage in bacteria. J Gen Microbiol. 1963;32(2):171–176. doi:10.1099/00221287-32-2-171.
   PubMedGoogle Scholar
• Lindner JG, Marcelis JH, de Vos NM, Hoogkamp-Korstanje JA, De Vos NM. Intracellular polysaccharide of Bacteroides fragilis. J Gen Microbiol. 1979;111(1):93–99. doi:10.1099/00221287-111-1-93.
   PubMedGoogle Scholar
• Marr AG, Nilson EH, Clark DJ. The maintenance requirement of Escherichia coli. Ann N Y Acad Sci. 1963;102(3):536–548. doi:10.1111/j.1749-6632.1963.tb13659.x.
   Web of Science ®Google Scholar
• Mallette MF. Validity of the concept of energy of maintenance. Ann N Y Acad Sci. 1963;102(3):521–535. doi:10.1111/j.1749-6632.1963.tb13658.x.
   PubMed Web of Science ®Google Scholar
• Gronlund AF, Campbell JJ. Nitrogenous substrates of endogenous respiration in Pseudomonas Aeruginosa. J Bacteriol. 1963;86(1):58–66. doi:10.1128/jb.86.1.58-66.1963.
   PubMed Web of Science ®Google Scholar
• Almagro G, Viale AM, Montero M, Rahimpour M, Munoz FJ, Baroja-Fernandez E, Bahaji A, Zúñiga M, González-Candelas F, Pozueta-Romero J, et al. Comparative genomic and phylogenetic analyses of Gammaproteobacterial glg genes traced the origin of the Escherichia coli glycogen glgBXCAP operon to the last common ancestor of the sister orders Enterobacteriales and Pasteurellales. PLoS One. 2015;10(1):e0115516. doi:10.1371/journal.pone.0115516.
   PubMed Web of Science ®Google Scholar
• Patel GB, Breuil C. Accumulation of an iodophilic polysaccharide during growth of Acetivibrio cellulolyticus on cellobiose. Arch Microbiol. 1981;129(4):265–267. doi:10.1007/BF00414695.
   Web of Science ®Google Scholar
• Shaw DH, Squires MJ. Optional production and utilization of polysaccharide by Aeromonas hydrophila. Arch Microbiol. 1980;125(1–2):83–87. doi:10.1007/BF00403202.
   PubMed Web of Science ®Google Scholar
• Strange RE. Induced enzyme synthesis in aqueous suspensions of starved stationary phase aerobacter aerogenes. Nature. 1961;191(4795):1272–1273. doi:10.1038/1911272a0.
   PubMedGoogle Scholar
• Barry C, Gavard R, Milhaud G, Aubert JP. The glycogen of Bacillus megatherium. C R Hebd Seances Acad Sci. 1952;235:1062–1064.
   PubMedGoogle Scholar
• Kiel JA, Boels JM, Beldman G, Venema G. Glycogen in Bacillus subtilis: molecular characterization of an operon encoding enzymes involved in glycogen biosynthesis and degradation. Mol Microbiol. 1994;11(1):203–218. doi:10.1111/j.1365-2958.1994.tb00301.x.
   PubMed Web of Science ®Google Scholar
• Whyte JN, Strasdine GA. An intracellular alpha-D-glucan from Clostridium botulinum, type E. Carbohydr Res. 1972;25(2):435–441. doi:10.1016/S0008-6215(00)81655-9.
   PubMed Web of Science ®Google Scholar
• Seibold GM, Eikmanns BJ. Inactivation of the phosphoglucomutase gene pgm in Corynebacterium glutamicum affects cell shape and glycogen metabolism. Biosci Rep. 2013;33(4). doi:10.1042/BSR20130076.
   PubMedGoogle Scholar
• Seibold GM, Breitinger KJ, Kempkes R, Both L, Kramer M, Dempf S, Eikmanns BJ. The glgB-encoded glycogen branching enzyme is essential for glycogen accumulation in Corynebacterium glutamicum. Microbiology. 2011;157(11):3243–3251. doi:10.1099/mic.0.051565-0.
   PubMedGoogle Scholar
• Holme T, Palmstierna H. Changes in glycogen and nitrogen-containing compounds in Escherichia coli b during growth in deficient media. I. Nitrogen and Carbon Starvation. Acta Chem Scan.1956;10:578–586.
   Google Scholar
• Fung T, Kwong N, van der Zwan T, Wu M. Residual glycogen metabolism in Escherichia coli is specific to the limiting macronutrient and varies during stationary phase. J Exp Microbiol Immunol. 2013;17:83–87.
   Google Scholar
• Wang L, Liu Q, Tan X, Wang Z, Wang M, Wise MJ, Li C, Ma C, Li E, Deng B, et al. Molecular structure of glycogen in Escherichia coli. Biomacromolecules. 2019;20(7):2821–2829. doi:10.1021/acs.biomac.9b00586.
   PubMed Web of Science ®Google Scholar
• Stewart CS, Paniagua C, Dinsdale D, Cheng KJ, Garrow SH. Selective isolation and characteristics of Bacteriodes succinogenes from the rumen of a cow. Appl Environ Microb. 1981;41(2):504–510. doi:10.1128/aem.41.2.504-510.1981.
   PubMed Web of Science ®Google Scholar
• Gaudet G, Forano E, Dauphin G, Delort AM. Futile cycling of glycogen in Fibrobacter succinogenes as shown by in situ 1H-NMR and 13C-NMR investigation. Eur J Biochem. 1992;207(1):155–162. doi:10.1111/j.1432-1033.1992.tb17032.x.
   PubMedGoogle Scholar
• Goh YJ, Klaenhammer TR. A functional glycogen biosynthesis pathway in Lactobacillus acidophilus: expression and analysis of the glg operon. Mol Microbiol. 2013;89(6):1187–1200. doi:10.1111/mmi.12338.
   PubMed Web of Science ®Google Scholar
• Cheng KJ, Hironaka R, Roberts DWA, Costerton JW. Cytoplasmic glycogen inclusions in cells of anaerobic gram-negative rumen bacteria. Can J Microbiol. 1973;19(12):1501–1506. doi:10.1139/m73-244.
   PubMed Web of Science ®Google Scholar
• Lou J, Dawson KA, Strobel HJ. Glycogen formation by the ruminal bacterium prevotella ruminicola. Appl Environ Microb. 1997;63(4):1483–1488. doi:10.1128/aem.63.4.1483-1488.1997.
   PubMed Web of Science ®Google Scholar
• Cheng KJ, Brown RG, Costerton JW. Characterization of a cytoplasmic reserve glucan from ruminococcus albus. Appl Environ Microbiol. 1977;33(3):718–724. doi:10.1128/aem.33.3.718-724.1977.
   PubMed Web of Science ®Google Scholar
• Bonafonte MA, Solano C, Sesma B, Alvarez M, Montuenga L, García-Ros D, Gamazo C. The relationship between glycogen synthesis, biofilm formation and virulence in Salmonella enteritidis. FEMS Microbiol Lett. 2000;191(1):31–36. doi:10.1111/j.1574-6968.2000.tb09315.x.
   PubMed Web of Science ®Google Scholar
• Kamio Y, Terawaki Y, Nakajima T, Matsuda K. Structure of glycogen produced by selenomonas ruminantium. Agric Biol Chem. 1981;45(1):209–216. doi:10.1271/bbb1961.45.209.
   Web of Science ®Google Scholar
• Wallace RJ. Cytoplasmic reserve polysaccharide of Selenomonas ruminantium. Appl Environ Microb. 1980;39(3):630. doi:10.1128/aem.39.3.630-634.1980.
   PubMed Web of Science ®Google Scholar
• McFarland CR, Snyder TL, McKenzie R. Polysaccharide storage in different streptococci. Microbios. 1984;40:7–14.
   PubMedGoogle Scholar
• van Houte J, Jansen HM. Role of glycogen in survival of Streptococcus mitis. J Bacteriol. 1970;101(3):1083–1085. doi:10.1128/jb.101.3.1083-1085.1970.
   PubMed Web of Science ®Google Scholar
• Bourassa L, Camilli A. Glycogen contributes to the environmental persistence and transmission of Vibrio cholerae. Mol Microbiol. 2009;72(1):124–138. doi:10.1111/j.1365-2958.2009.06629.x.
   PubMed Web of Science ®Google Scholar
• Preiss J. Bacterial glycogen synthesis and its regulation. Annu Rev Microbiol. 1984;38(1):419–458. doi:10.1146/annurev.mi.38.100184.002223.
   PubMedGoogle Scholar
• Preiss J, Romeo T. Physiology, biochemistry and genetics of bacterial glycogen synthesis. Adv Microb Physiol. 1989;30:183–238.
   PubMed Web of Science ®Google Scholar
• Dawes EA, Ribbons DW. Studies on the endogenous metabolism of Escherichia coli. Biochem J. 1965;95(2):332–343. doi:10.1042/bj0950332.
   PubMed Web of Science ®Google Scholar
• Klotz A, Forchhammer K. Glycogen, a major player for bacterial survival and awakening from dormancy. Future Microbiol. 2017;12(2):101–104. doi:10.2217/fmb-2016-0218.
   PubMed Web of Science ®Google Scholar
• Henrissat B, Deleury E, Coutinho PM. Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria? Trends Genet. 2002;18(9):437–440. doi:10.1016/S0168-9525(02)02734-8.
   PubMed Web of Science ®Google Scholar
• Preiss J. Bacterial glycogen inclusions: enzymology and regulation of synthesis. In: Shively J, editor. Inclusions in prokaryotes. Berlin, HeidelbergBerlin Heidelberg:Springer; 2006. pp. 71–108. doi:10.1007/3-540-33774-1_4.
   Google Scholar
• Alonso-Casajus N, Dauvillee D, Viale AM, Munoz FJ, Baroja-Fernandez E, Moran-Zorzano MT, Eydallin G, Ball S, Pozueta-Romero J. Glycogen phosphorylase, the product of the glgP Gene, catalyzes glycogen breakdown by removing glucose units from the nonreducing ends in Escherichia coli. J Bacteriol. 2006;188(14):5266–5272. doi:10.1128/JB.01566-05.
   PubMed Web of Science ®Google Scholar
• Dauvillee D, Kinderf IS, Li Z, Kosar-Hashemi B, Samuel MS, Rampling L, Ball S, Morell MK. Role of the Escherichia coli glgX gene in glycogen metabolism. J Bacteriol. 2005;187(4):1465–1473. doi:10.1128/JB.187.4.1465-1473.2005.
   PubMed Web of Science ®Google Scholar
• O’Callaghan A, van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol. 2016;7:925.
   Google Scholar
• Schneider D, Bruton CJ, Chater KF. Duplicated gene clusters suggest an interplay of glycogen and trehalose metabolism during sequential stages of aerial mycelium development in Streptomyces coelicolor A3(2). Mol Gen Genet. 2000;263(3):543–553. doi:10.1007/s004380051200.
   PubMedGoogle Scholar
• Chandra G, Chater KF, Bornemann S. Unexpected and widespread connections between bacterial glycogen and trehalose metabolism. Microbiology. 2011;157(6):1565–1572. doi:10.1099/mic.0.044263-0.
   PubMedGoogle Scholar
• Park JT, Shim JH, Tran PL, Hong IH, Yong HU, Oktavina EF, Nguyen HD, Kim J-W, Lee TS, Park S-H, et al. Role of maltose enzymes in glycogen synthesis by Escherichia coli. J Bacteriol. 2011;193(10):2517–2526. doi:10.1128/JB.01238-10.
   PubMed Web of Science ®Google Scholar
• Wang L, Wise MJ. Glycogen with short average chain length enhances bacterial durability. Naturwissenschaften. 2011;98(9):719–729. doi:10.1007/s00114-011-0832-x.
   PubMedGoogle Scholar
• Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015;16(1):51. doi:10.1186/s13059-015-0611-7.
   PubMedGoogle Scholar
• Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328(5981):994–999. doi:10.1126/science.1183605.
   PubMed Web of Science ®Google Scholar
• Milani C, Lugli GA, Duranti S, Turroni F, Mancabelli L, Ferrario C, Mangifesta M, Hevia A, Viappiani A, Scholz M, et al. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep. 2015;5(1):15782. doi:10.1038/srep15782.
   PubMedGoogle Scholar
• Pasolli E, De Filippis F, Mauriello IE, Cumbo F, Walsh AM, Leech J, Cotter PD, Segata N, Ercolini D. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat Commun. 2020;11(1):2610. doi:10.1038/s41467-020-16438-8.
   PubMed Web of Science ®Google Scholar
• Kaznadzey A, Shelyakin P, Belousova E, Eremina A, Shvyreva U, Bykova D, Emelianenko V, Korosteleva A, Tutukina M, Gelfand MS, et al. The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation. Sci Rep. 2018;8(1):3177. doi:10.1038/s41598-018-21534-3.
   PubMedGoogle Scholar
• Romeo T, Black J, Preiss J. Genetic regulation of glycogen biosynthesis inEscherichia coli: In vivo effects of the catabolite repression and stringent response systems inglg gene expression. Curr Microbiol. 1990;21(2):131–137. doi:10.1007/BF02091831.
   Web of Science ®Google Scholar
• Takata H, Takaha T, Okada S, Takagi M, Imanaka T. Characterization of a gene cluster for glycogen biosynthesis and a heterotetrameric ADP-glucose pyrophosphorylase from Bacillus stearothermophilus. J Bacteriol. 1997;179(15):4689–4698. doi:10.1128/jb.179.15.4689-4698.1997.
   PubMed Web of Science ®Google Scholar
• Görke B, Stülke J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol. 2008;6(8):613–624. doi:10.1038/nrmicro1932.
   PubMed Web of Science ®Google Scholar
• Barrangou R, Azcarate-Peril MA, Duong T, Conners SB, Kelly RM, Klaenhammer TR. Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays. Proc Natl Acad Sci USA. 2006;103(10):3816. doi:10.1073/pnas.0511287103.
   PubMed Web of Science ®Google Scholar
• Handtke S, Albrecht D, Otto A, Becher D, Hecker M, Voigt B. The proteomic response of bacillus pumilus cells to glucose starvation. Proteomics. 2018;18(1):1700109. doi:10.1002/pmic.201700109.
   Web of Science ®Google Scholar
• Montero M, Eydallin G, Viale Alejandro A, Almagro G, Muñoz Francisco F, Rahimpour M, Sesma M, Baroja-Fernández E, Pozueta-Romero J. Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes. Biochem J. 2009;424(1):129–141. doi:10.1042/BJ20090980.
   PubMedGoogle Scholar
• Ronneau S, Hallez R. Make and break the alarmone: regulation of (p)ppGpp synthetase/hydrolase enzymes in bacteria. FEMS Microbiol Rev. 2019;43(4):389–400. doi:10.1093/femsre/fuz009.
   PubMed Web of Science ®Google Scholar
• Durfee T, Hansen A-M, Zhi H, Blattner FR, Jin DJ. Transcription profiling of the stringent response in Escherichia coli. J Bacteriol. 2008;190(3):1084. doi:10.1128/JB.01092-07.
   PubMed Web of Science ®Google Scholar
• Magnusson LU, Farewell A, Nyström T. ppGpp: a global regulator in Escherichia coli. Trends Microbiol. 2005;13(5):236–242. doi:10.1016/j.tim.2005.03.008.
   PubMed Web of Science ®Google Scholar
• Britton RA, Eichenberger P, Gonzalez-Pastor JE, Fawcett P, Monson R, Losick R, Grossman AD. Genome-wide analysis of the stationary-phase sigma factor (Sigma-H) Regulon of Bacillus subtilis. J Bacteriol. 2002;184(17):4881. doi:10.1128/JB.184.17.4881-4890.2002.
   PubMed Web of Science ®Google Scholar
• Slauch J, Taylor R, Maloy S. Survival in a cruel world: how Vibrio cholerae and Salmonella respond to an unwilling host. Genes Dev. 1997;11(14):1761–1774. doi:10.1101/gad.11.14.1761.
   PubMed Web of Science ®Google Scholar
• Liu MY, Gui G, Wei B, Preston JF, Oakford L, Yüksel Ü, Giedroc DP, Romeo T. The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem. 1997;272(28):17502–17510. doi:10.1074/jbc.272.28.17502.
   PubMed Web of Science ®Google Scholar
• Berndt V, Beckstette M, Volk M, Dersch P, Bronstrup M. Metabolome and transcriptome-wide effects of the carbon storage regulator a in enteropathogenic Escherichia coli. Sci Rep. 2019;9(1):138. doi:10.1038/s41598-018-36932-w.
   PubMedGoogle Scholar
• Romeo T. Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB. Mol Microbiol. 1998;29(6):1321–1330. doi:10.1046/j.1365-2958.1998.01021.x.
   PubMed Web of Science ®Google Scholar
• Liaw SJ, Lai HC, Ho SW, Luh KT, Wang WB. Role of RsmA in the regulation of swarming motility and virulence factor expression in Proteus mirabilis. J Med Microbiol. 2003;52(Pt 1):19–28. doi:10.1099/jmm.0.05024-0.
   PubMed Web of Science ®Google Scholar
• Preiss J. Regulation of adenosine diphosphate glucose pyrophosphorylase. Adv Enzymol Relat Areas Mol Biol. 1978;46:317–381.
   PubMedGoogle Scholar
• Asención Diez MD, Demonte AM, Syson K, Arias DG, Gorelik A, Guerrero SA, Bornemann S, Iglesias AA. Allosteric regulation of the partitioning of glucose-1-phosphate between glycogen and trehalose biosynthesis in Mycobacterium tuberculosis. Biochim et Biophys Acta (BBA) - Gen Subj. 2015;1850(1):13–21. doi:10.1016/j.bbagen.2014.09.023.
   PubMed Web of Science ®Google Scholar
• Cereijo AE, Asencion Diez MD, Ballicora MA, Iglesias AA, Metcalf WW. Regulatory properties of the ADP-glucose pyrophosphorylase from the clostridial firmicutes member ruminococcus albus. J Bacteriol. 2018;200(17). doi:10.1128/JB.00172-18.
   PubMed Web of Science ®Google Scholar
• Ballicora MA, Iglesias AA, Preiss J. ADP-glucose pyrophosphorylase, a regulatory enzyme for bacterial glycogen synthesis. Microbiol Mol Biol R. 2003;67(2):213. doi:10.1128/MMBR.67.2.213-225.2003.
   PubMed Web of Science ®Google Scholar
• Yung SG, Paule M, Beggs R, Greenberg E, Preiss J. Biosynthesis of bacterial glycogen: characterization of adenosine diphosphate glucose synthetases from Enterobacter hafniae and Aeromonas hydrophila. Arch Microbiol. 1984;138(1):1–8. doi:10.1007/BF00425398.
   PubMed Web of Science ®Google Scholar
• Hengge-Aronis R, Fischer D. Identification and molecular analysis of glgS, a novel growth-phase-regulated and rpoS-dependent gene involved in glycogen synthesis in Escherichia coli. Mol Microbiol. 1992;6(14):1877–1886. doi:10.1111/j.1365-2958.1992.tb01360.x.
   PubMed Web of Science ®Google Scholar
• Sekar K, Linker SM, Nguyen J, Grünhagen A, Stocker R, Sauer U, Cann I. Bacterial glycogen provides short-term benefits in changing environments. Appl Environ Microb. 2020;86(9):e00049–20. doi:10.1128/AEM.00049-20.
   PubMed Web of Science ®Google Scholar
• Cassani L, Gomez-Zavaglia A, Simal-Gandara J. Technological strategies ensuring the safe arrival of beneficial microorganisms to the gut: From food processing and storage to their passage through the gastrointestinal tract. Food Res Int. 2020;129:108852. doi:10.1016/j.foodres.2019.108852.
   PubMed Web of Science ®Google Scholar
• Merritt ME, Donaldson JR. Effect of bile salts on the DNA and membrane integrity of enteric bacteria. J Med Microbiol. 2009;58(12):1533–1541. doi:10.1099/jmm.0.014092-0.
   PubMed Web of Science ®Google Scholar
• Finkel SE. Long-term survival during stationary phase: evolution and the GASP phenotype. Nat Rev Microbiol. 2006;4(2):113–120. doi:10.1038/nrmicro1340.
   PubMed Web of Science ®Google Scholar
• Kaczmarek JL, Thompson SV, Holscher HD. Complex interactions of circadian rhythms, eating behaviors, and the gastrointestinal microbiota and their potential impact on health. Nutr Rev. 2017;75(9):673–682. doi:10.1093/nutrit/nux036.
   PubMed Web of Science ®Google Scholar
• Koch AL. The adaptive responses of Escherichia coli to a feast and famine existence. Adv Microb Physiol. 1971;6:147–217.
   PubMedGoogle Scholar
• Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 2016;14(1):20–32. doi:10.1038/nrmicro3552.
   PubMed Web of Science ®Google Scholar
• De Paepe M, Gaboriau-Routhiau V, Rainteau D, Rakotobe S, Taddei F, Cerf-Bensussan N, Casadesús J. Trade-off between bile resistance and nutritional competence drives Escherichia coli diversification in the mouse gut. PLoS Genet. 2011;7(6):e1002107–e. doi:10.1371/journal.pgen.1002107.
   PubMed Web of Science ®Google Scholar
• Strange RE. Bacterial “glycogen” and survival. Nature. 1968;220(5167):606–607. doi:10.1038/220606a0.
   PubMed Web of Science ®Google Scholar
• Zartl B, Silberbauer K, Loeppert R, Viernstein H, Praznik W, Mueller M. Fermentation of non-digestible raffinose family oligosaccharides and galactomannans by probiotics. Food Funct. 2018;9(3):1638–1646. doi:10.1039/C7FO01887H.
   PubMed Web of Science ®Google Scholar
• Hernandez MA, Mohn WW, Martinez E, Rost E, Alvarez AF, Alvarez HM. Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism. Bmc Genom. 2008;9(1):600. doi:10.1186/1471-2164-9-600.
   PubMedGoogle Scholar
• Olga Z, Alexander Z, Kathleen R, Trissa B, John A. Host stress and virulence expression in intestinal pathogens: development of therapeutic strategies using mice and C. elegans. Curr Pharm Des. 2011;17(13):1254–1260. doi:10.2174/138161211795703771.
   PubMed Web of Science ®Google Scholar
• Reese AT, Pereira FC, Schintlmeister A, Berry D, Wagner M, Hale LP, Wu A, Jiang S, Durand HK, Zhou X, et al. Microbial nitrogen limitation in the mammalian large intestine. Nature Microbiology. 2018;3(12):1441–1450. doi:10.1038/s41564-018-0267-7.
   PubMed Web of Science ®Google Scholar
• Holmes AJ, Chew YV, Colakoglu F, Cliff JB, Klaassens E, Read MN, Solon-Biet SM, McMahon AC, Cogger VC, Ruohonen K, et al. Diet-microbiome interactions in health are controlled by intestinal nitrogen source constraints. Cell Metab. 2017;25(1):140–151. doi:10.1016/j.cmet.2016.10.021.
   PubMed Web of Science ®Google Scholar
• Eydallin G, Viale AM, Moran-Zorzano MT, Munoz FJ, Montero M, Baroja-Fernandez E, Pozueta-Romero J. Genome-wide screening of genes affecting glycogen metabolism in Escherichia coli K-12. FEBS Lett. 2007;581(16):2947–2953. doi:10.1016/j.febslet.2007.05.044.
   PubMed Web of Science ®Google Scholar
• Vinella D, Albrecht C, Cashel M, D’Ari R. Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli. Mol Microbiol. 2005;56(4):958–970. doi:10.1111/j.1365-2958.2005.04601.x.
   PubMed Web of Science ®Google Scholar
• Lanigan N, Bottacini F, Casey PG, O’Connell Motherway M, van Sinderen D. Genome-wide search for genes required for bifidobacterial growth under iron-limitation. Front Microbiol. 2017;8:964. doi:10.3389/fmicb.2017.00964.
   PubMed Web of Science ®Google Scholar
• Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L. Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol. 2010;6(1):364. doi:10.1038/msb.2010.18.
   PubMedGoogle Scholar
• Svensater G, Bjornsson O, Hamilton IR. Effect of carbon starvation and proteolytic activity on stationary-phase acid tolerance of Streptococcus mutans. Microbiology. 2001;147(Pt 11):2971–2979. doi:10.1099/00221287-147-11-2971.
   PubMedGoogle Scholar
• Buchanan R, Doyle MP. Foodborne disease significance of Escherichia coli O157: H7 and other enterohemorrhagic E. coli. Food Technol. 1997;51:69–76.
   Web of Science ®Google Scholar
• Hamilton IR, Buckley ND. Adaptation by Streptococcus mutans to acid tolerance. Oral Microbiol Immunol. 1991;6(2):65–71. doi:10.1111/j.1399-302X.1991.tb00453.x.
   PubMedGoogle Scholar
• Papadimitriou K, Alegria A, Bron PA, de Angelis M, Gobbetti M, Kleerebezem M, Lemos JA, Linares DM, Ross P, Stanton C, et al. Stress physiology of lactic acid bacteria. Microbiol Mol Biol Rev. 2016;80(3):837–890. doi:10.1128/MMBR.00076-15.
   PubMed Web of Science ®Google Scholar
• Baucheron S, Nishino K, Monchaux I, Canepa S, Maurel M-C, Coste F, Roussel A, Cloeckaert A, Giraud E. Bile-mediated activation of the acrAB and tolC multidrug efflux genes occurs mainly through transcriptional derepression of ramA in Salmonella enterica serovar Typhimurium. J Antimicrob Chemother. 2014;69(9):2400–2406. doi:10.1093/jac/dku140.
   PubMed Web of Science ®Google Scholar
• Seibold GM, Hagmann CT, Schietzel M, Emer D, Auchter M, Schreiner J, Eikmanns BJ. The transcriptional regulators RamA and RamB are involved in the regulation of glycogen synthesis in Corynebacterium glutamicum. Microbiology. 2010;156(4):1256–1263. doi:10.1099/mic.0.036756-0.
   PubMedGoogle Scholar
• Buret AG, Motta J-P, Allain T, Ferraz J, Wallace JL. Pathobiont release from dysbiotic gut microbiota biofilms in intestinal inflammatory diseases: a role for iron? J Biomed Sci. 2019;26(1):1. doi:10.1186/s12929-018-0495-4.
   PubMed Web of Science ®Google Scholar
• Jackson DW, Suzuki K, Oakford L, Simecka JW, Hart ME, Romeo T. Biofilm Formation and Dispersal under the Influence of the Global Regulator CsrA of Escherichia coli. J Bacteriol. 2002;184(1):290. doi:10.1128/JB.184.1.290-301.2002.
   PubMed Web of Science ®Google Scholar
• Montanez ND, Carreno H, Escobar P, Estupinan HA, Pena DY, Goel S, Endrino JL. Functional evaluation and testing of a newly developed teleost’s fish otolith derived biocomposite coating for healthcare. Sci Rep. 2020;10(1):258. doi:10.1038/s41598-019-57128-w.
   PubMed Web of Science ®Google Scholar
• Kelly SM, Lanigan N, O’Neill IJ, Bottacini F, Lugli GA, Viappiani A, Turroni F, Ventura M, van Sinderen D. Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure. Sci Rep. 2020;10(1):11598. doi:10.1038/s41598-020-68179-9.
   PubMed Web of Science ®Google Scholar
• Rahimpour M, Montero M, Almagro G, Viale Alejandro M, Sevilla Á, Cánovas M, Muñoz F, Baroja-Fernández E, Bahaji A, Eydallin G, et al. GlgS, described previously as a glycogen synthesis control protein, negatively regulates motility and biofilm formation in Escherichia coli. Biochem J. 2013;452(3):559–573. doi:10.1042/BJ20130154.
   PubMedGoogle Scholar
• Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, et al. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology. 2016;1(10):16131. doi:10.1038/nmicrobiol.2016.131.
   PubMed Web of Science ®Google Scholar
• Wu M, McNulty NP, Rodionov DA, Khoroshkin MS, Griffin NW, Cheng J, Latreille P, Kerstetter RA, Terrapon N; Henrissat B et al. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science. 2015;350(6256):aac5992.
   Google Scholar
• Mann E, Wetzels SU, Wagner M, Zebeli Q, Schmitz-Esser S. Metatranscriptome sequencing reveals insights into the gene expression and functional potential of rumen wall bacteria. Front Microbiol. 2018;9:43. doi:10.3389/fmicb.2018.00043.
   PubMed Web of Science ®Google Scholar
• Esteban-Torres M, Santamaria L, Cabrera-Rubio R, Plaza-Vinuesa L, Crispie F, de Las Rivas B, Cotter P, Muñoz R. A diverse range of human gut bacteria have the potential to metabolize the dietary component gallic acid. Appl Environ Microbiol. 2018;84(19). doi:10.1128/AEM.01558-18.
   PubMed Web of Science ®Google Scholar
• Walker AW, Duncan SH, Louis P, Flint HJ. Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol. 2014;22(5):267–274. doi:10.1016/j.tim.2014.03.001.
   PubMed Web of Science ®Google Scholar
• van der Maarel MJ, Leemhuis H, van der Maarel MJEC. Starch modification with microbial alpha-glucanotransferase enzymes. Carbohydr Polym. 2013;93(1):116–121. doi:10.1016/j.carbpol.2012.01.065.
   PubMed Web of Science ®Google Scholar
• Lee S, Cantarel B, Henrissat B, Gevers D, Birren BW, Huttenhower C, Ko G. Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. Isme J. 2014;8(3):493–503. doi:10.1038/ismej.2013.167.
   PubMed Web of Science ®Google Scholar
• Ranjan R, Rani A, Finn PW, Perkins DL. Multiomic strategies reveal diversity and important functional aspects of human gut microbiome. Biomed Res Int. 2018;2018:1–13. doi:10.1155/2018/6074918.
   Web of Science ®Google Scholar
• Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, et al. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nature Microbiology. 2018;3(3):356–366. doi:10.1038/s41564-017-0084-4.
   PubMed Web of Science ®Google Scholar
• Gosalbes MJ, Compte J, Moriano-Gutierrez S, Valles Y, Jimenez-Hernandez N, Pons X, Artacho A, Francino MP. Metabolic adaptation in the human gut microbiota during pregnancy and the first year of life. EBioMedicine. 2019;39:497–509. doi:10.1016/j.ebiom.2018.10.071.
   PubMed Web of Science ®Google Scholar
• McMeechan A, Lovell MA, Cogan TA, Marston KL, Humphrey TJ, Barrow PA. Glycogen production by different Salmonella enterica serotypes: contribution of functional glgC to virulence, intestinal colonization and environmental survival. Microbiology. 2005;151(12):3969–3977. doi:10.1099/mic.0.28292-0.
   PubMedGoogle Scholar
• Janoir C, Deneve C, Bouttier S, Barbut F, Hoys S, Caleechum L, Chapetón-Montes D, Pereira FC, Henriques AO, Collignon A, et al. Adaptive strategies and pathogenesis of Clostridium difficile from in vivo transcriptomics. Infect Immun. 2013;81(10):3757–3769. doi:10.1128/IAI.00515-13.
   PubMed Web of Science ®Google Scholar
• Hasan MK. Role of glycogen and cellobiose PTS operon in clostridiodes difficile virulence and pathogenesis. Kansas State University; 2019.
   Google Scholar
• Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D, Lawley TD. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature. 2016;533(7604):543–546. doi:10.1038/nature17645.
   PubMed Web of Science ®Google Scholar
• Dietzler DN, Leckie MP, Lais CJ, Henry DA, Rothert JH, Ferguson RM. Periodic inventory review as a strategy for survival in Escherichia coli. The observation of precisely timed, rapid, and simultaneous shifts in glycogen synthesis and glucose utilization in the absence of an external stimulus during prolonged nitrogen starvation. J Biol Chem. 1979;254:8288–8294.
   PubMed Web of Science ®Google Scholar