The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging – relevant neural and immune function

References

• Hill JH, Round JL. SnapShot: microbiota effects on host physiology. Cell. 2021;184(10):1–22 . doi:10.1016/j.cell.2021.04.026.
   PubMed Web of Science ®Google Scholar
• Biagi E, Franceschi C, Rampelli S, Severgnini M, Ostan R, Turroni S, Consolandi C, Quercia S, Scurti M, Monti D, et al. Gut microbiota and extreme longevity. Curr Biol. 2016;26(11):1480–1485. doi:10.1016/j.cub.2016.04.016.
   PubMed Web of Science ®Google Scholar
• Kong F, Deng F, Li Y, Zhao J. Identification of gut microbiome signatures associated with longevity provides a promising modulation target for healthy aging. Gut Microbes. 2019;10(2):210–215. doi:10.1080/19490976.2018.1494102.
   PubMed Web of Science ®Google Scholar
• Luan Z, Sun G, Huang Y, Yang Y, Yang R, Li C, Wang T, Di T, Qi S, Jun C, et al. Metagenomics study reveals changes in gut microbiota in centenarians: a cohort study of hainan centenarians. Front Microbiol. 2020;11:1474. doi:10.3389/fmicb.2020.01474.
   PubMed Web of Science ®Google Scholar
• Wu L, Zeng T, Zinellu A, Rubino S, Kelvin DJ, Carru C . A cross-sectional study of compositional and functional profiles of gut microbiota in sardinian centenarians. mSystems. 2019;4(4): e00325–19. doi:10.1128/mSystems.00325-19.
   PubMed Web of Science ®Google Scholar
• Kong F, Hua Y, Zeng B, Ning R, Li Y, Zhao J. Gut microbiota signatures of longevity. Curr Biol. 2016;26(18):R832–R3. doi:10.1016/j.cub.2016.08.015.
   PubMed Web of Science ®Google Scholar
• Wang N, Li R, Lin H, Fu C, Wang X, Zhang Y, Su M, Huang P, Qian J, Jiang F, et al. Enriched taxa were found among the gut microbiota of centenarians in East China. PLoS One. 2019;14(10):e0222763. doi:10.1371/journal.pone.0222763.
   PubMed Web of Science ®Google Scholar
• Yao Y, Cai X, Fei W, Ye Y, Zhao M, Zheng C. The role of short-chain fatty acids in immunity, inflammation and metabolism. Crit Rev Food Sci Nutr. 2022;62(1):1–12. doi:10.1080/10408398.2020.1854675.
   PubMed Web of Science ®Google Scholar
• Park JS, Shin E, Hong H, Shin HJ, Cho YH, Ahn KH, Paek K, Lee Y. Characterization of lactobacillus fermentum PL9988 isolated from healthy elderly Korean in a longevity village. J Microbiol Biotechnol. 2015;25(9):1510–1518. doi:10.4014/jmb.1505.05015.
   PubMed Web of Science ®Google Scholar
• Agirman G, Yu KB, Hsiao EY. Signaling inflammation across the gut-brain axis. Science. 2021;374(6571):1087–1092. doi:10.1126/science.abi6087.
   PubMed Web of Science ®Google Scholar
• Cryan JF, O’Riordan KJ, Sandhu K, Peterson V, Dinan TG. The gut microbiome in neurological disorders. Lancet Neurol. 2020;19(2):179–194. doi:10.1016/S1474-4422(19)30356-4.
   PubMed Web of Science ®Google Scholar
• Han B, Sivaramakrishnan P, Lin CJ, Neve IAA, He J, Tay LWR, Sowa JN, Sizovs A, Du G, Wang J, et al. Microbial genetic composition tunes host longevity. Cell. 2017;169(7):1249–62 e13. doi:10.1016/j.cell.2017.05.036.
   PubMed Web of Science ®Google Scholar
• Chen L, Wang D, Garmaeva S, Kurilshikov A, Vich Vila A, Gacesa R, Sinha T, Segal E, Weersma RK, Wijmenga C, et al. The long-term genetic stability and individual specificity of the human gut microbiome. Cell. 2021;184(9):2302–15 e12. doi:10.1016/j.cell.2021.03.024.
   PubMed Web of Science ®Google Scholar
• Tao Y, Yimiti D, Yasen B, Z XY, M XM, Mahemuti B. Analysis of intestinal flora diversity in long-lived elderly people of Xinjiang Uyghur. Journal of Pathogen Biology. 2009;4:271–274.
   Google Scholar
• Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S, et al. Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature. 2021;599(7885):458–464. doi:10.1038/s41586-021-03832-5.
   PubMed Web of Science ®Google Scholar
• Lei Y, Tang L, Liu S, Hu S, Wu L, Liu Y, Yang M, Huang S, Tang X, Tang T, et al. Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration. Microbiome. 2021;9(1):115. doi:10.1186/s40168-021-01065-2.
   PubMed Web of Science ®Google Scholar
• Lima SF, Gogokhia L, Viladomiu M, Chou L, Putzel G, Jin WB, Pires S, Guo C-J, Gerardin Y, Crawford CV, et al. Transferable immunoglobulin A-coated odoribacter splanchnicus in responders to fecal microbiota transplantation for ulcerative colitis limits colonic inflammation. Gastroenterology. 2022;162(1):166–178. doi:10.1053/j.gastro.2021.09.061.
   PubMed Web of Science ®Google Scholar
• Zhang CH, Yin AH, Li HD, Wang RR, Wu GJ, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, et al. Dietary modulation of gut microbiota contributes to alleviation of both genetic and simple obesity in children. Ebiomedicine. 2015;2(8):968–984. doi:10.1016/j.ebiom.2015.07.007.
   PubMed Web of Science ®Google Scholar
• Zhao LP, Zhang F, Ding XY, Wu GJ, Lam YY, Wang XJ, Fu H, Xue X, Lu C, Ma J, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science. 2018;359(6380):1151–+. doi:10.1126/science.aao5774.
   PubMed Web of Science ®Google Scholar
• Uritskiy GV, DiRuggiero J, Taylor J, Zaidman-Rémy A, Heddi A. MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6(1):6. doi:10.1186/s40168-017-0397-9.
   PubMedGoogle Scholar
• Roth N, Kasbohrer A, Mayrhofer S, Zitz U, Hofacre C, Domig KJ. The application of antibiotics in broiler production and the resulting antibiotic resistance in Escherichia coli: a global overview. Poult Sci. 2019;98(4):1791–1804. doi:10.3382/ps/pey539.
   PubMed Web of Science ®Google Scholar
• Bian GR, Gloor GB, Gong AH, Jia CS, Zhang W, Hu J, Zhang H, Zhang Y, Zhou Z, Zhang J, et al. The gut microbiota of healthy aged Chinese is similar to that of the healthy young. Msphere. 2017;2(5). doi:10.1128/mSphere.00327-17.
   PubMed Web of Science ®Google Scholar
• Muller PA, Schneeberger M, Matheis F, Wang P, Kerner Z, Ilanges A, Pellegrino K, Del Mármol J, Castro TBR, Furuichi M, et al. Microbiota modulate sympathetic neurons via a gut-brain circuit. Nature. 2020;583(7816):441–446. doi:10.1038/s41586-020-2474-7.
   PubMed Web of Science ®Google Scholar
• Bathina S, Srinivas N, Das UN. BDNF protects pancreatic beta cells (RIN5F) against cytotoxic action of alloxan, streptozotocin, doxorubicin and benzo(a)pyrene in vitro. Metabolism. 2016;65(5):667–684. doi:10.1016/j.metabol.2016.01.016.
   PubMed Web of Science ®Google Scholar
• Romoli M, Sen A, Parnetti L, Calabresi P, Costa C. Amyloid-beta: a potential link between epilepsy and cognitive decline. Nat Rev Neurol. 2021;17(8):469–485. doi:10.1038/s41582-021-00505-9.
   PubMed Web of Science ®Google Scholar
• Perls T, Kunkel LM, Puca AA. The genetics of exceptional human longevity. J Am Geriatr Soc. 2002;50(2):359–368. doi:10.1046/j.1532-5415.2002.49283.x.
   PubMed Web of Science ®Google Scholar
• Chen P, Xu H, Tang H, Zhao F, Yang C, Kwok LY, Cong C, Wu Y, Zhang W, Zhou X, et al. Modulation of gut mucosal microbiota as a mechanism of probiotics-based adjunctive therapy for ulcerative colitis. Microb Biotechnol. 2020;13(6):2032–2043. doi:10.1111/1751-7915.13661.
   PubMed Web of Science ®Google Scholar
• Olm MR, Crits-Christoph A, Bouma-Gregson K, Firek BA, Morowitz MJ, Banfield JF. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat Biotechnol. 2021;39(6):727–+. doi:10.1038/s41587-020-00797-0.
   PubMed Web of Science ®Google Scholar
• Ctoi AF, Corina A, Katsiki N, Vodnar DC, Andreicut AD, Stoian AP, Rizzo M, Pérez-Martínez P. Gut microbiota and aging-A focus on centenarians. Biochim Biophys Acta Mol Basis Dis. 2020;1866(7):165765. doi:10.1016/j.bbadis.2020.165765.
   PubMed Web of Science ®Google Scholar
• Santoro A, Ostan R, Candela M, Biagi E, Brigidi P, Capri M, Franceschi C. Gut microbiota changes in the extreme decades of human life: a focus on centenarians. Cell Mol Life Sci. 2018;75(1):129–148. doi:10.1007/s00018-017-2674-y.
   PubMed Web of Science ®Google Scholar
• Clavel T, Gomes-Neto JC, Lagkouvardos I, Ramer-Tait AE. Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes. Immunol Rev. 2017;279(1):8–22. doi:10.1111/imr.12578.
   PubMed Web of Science ®Google Scholar
• Kim BS, Choi CW, Shin H, Jin SP, Bae JS, Han M, Seo EY, Chun J, Chung JH. Comparison of the gut microbiota of centenarians in longevity villages of South Korea with those of other age groups. J Microbiol Biotechnol. 2019;29(3):429–440. doi:10.4014/jmb.1811.11023.
   PubMed Web of Science ®Google Scholar
• Thevaranjan N, Puchta A, Schulz C, Naidoo A, Szamosi JC, Verschoor CP, Loukov D, Schenck LP, Jury J, Foley KP, et al. Age-associated microbial dysbiosis promotes intestinal permeability, systemic inflammation, and macrophage dysfunction. Cell Host Microbe. 2018;23(4):570. doi:10.1016/j.chom.2018.03.006.
   PubMed Web of Science ®Google Scholar
• Haran JP, McCormick BA. Aging, frailty, and the microbiome-how dysbiosis influences human aging and disease. Gastroenterology. 2021;160(2):507–523. doi:10.1053/j.gastro.2020.09.060.
   PubMed Web of Science ®Google Scholar
• Ansaldo E, Farley TK, Belkaid Y. Control of immunity by the microbiota. Annu Rev Immunol. 2021;39(1):449–479. doi:10.1146/annurev-immunol-093019-112348.
   PubMed Web of Science ®Google Scholar
• Ramakrishna C, Kujawski M, Chu H, Li L, Mazmanian SK, Cantin EM. Bacteroides fragilis polysaccharide A induces IL-10 secreting B and T cells that prevent viral encephalitis. Nat Commun. 2019;10(1):2153. doi:10.1038/s41467-019-09884-6.
   PubMedGoogle Scholar
• Telesford KM, Yan W, Ochoa-Reparaz J, Pant A, Kircher C, Christy MA, Begum-Haque S, Kasper DL, Kasper LH. A commensal symbiotic factor derived from Bacteroides fragilis promotes human CD39 + Foxp3 + T cells and T reg function. Gut Microbes. 2015;6(4):234–242. doi:10.1080/19490976.2015.1056973.
   PubMed Web of Science ®Google Scholar
• Sun MF, Shen YQ. Dysbiosis of gut microbiota and microbial metabolites in Parkinson’s disease. Ageing Res Rev. 2018;45:53–61. doi:10.1016/j.arr.2018.04.004.
   PubMed Web of Science ®Google Scholar
• Kesika P, Suganthy N, Sivamaruthi BS, Chaiyasut C. Role of gut-brain axis, gut microbial composition, and probiotic intervention in Alzheimer’s disease. Life Sci. 2021;264:118627. doi:10.1016/j.lfs.2020.118627.
   PubMed Web of Science ®Google Scholar
• Zhang K, Mizuma H, Zhang X, Takahashi K, Jin C, Song F, Gao Y, Kanayama Y, Wu Y, Li Y, et al. PET imaging of neural activity, beta-amyloid, and tau in normal brain aging. Eur J Nucl Med Mol Imaging. 2021;48(12):3859–3871. doi:10.1007/s00259-021-05230-5.
   PubMed Web of Science ®Google Scholar
• Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, Codagnone MG, Cussotto S, Fulling C, Golubeva AV, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99(4):1877–2013. doi:10.1152/physrev.00018.2018.
   PubMed Web of Science ®Google Scholar
• Moya-Perez A, Perez-Villalba A, Benitez-Paez A, Campillo I, Sanz Y. Bifidobacterium CECT 7765 modulates early stress-induced immune, neuroendocrine and behavioral alterations in mice. Brain Behav Immun. 2017;65:43–56. doi:10.1016/j.bbi.2017.05.011.
   PubMed Web of Science ®Google Scholar
• Key MN, Zwilling CE, Talukdar T, Barbey AK. Essential amino acids, vitamins, and minerals moderate the relationship between the right frontal pole and measures of memory. Mol Nutr Food Res. 2019;63(15):e1801048. doi:10.1002/mnfr.201801048.
   PubMed Web of Science ®Google Scholar
• Sun J, Zhang S, Zhang X, Zhang X, Dong H, Qian Y. IL-17A is implicated in lipopolysaccharide-induced neuroinflammation and cognitive impairment in aged rats via microglial activation. J Neuroinflammation. 2015;12(1):165. doi:10.1186/s12974-015-0394-5.
   PubMedGoogle Scholar
• Tian A, Ma H, Zhang R, Tan W, Wang X, Wu B, Wang J, Wan C. Interleukin17A promotes postoperative cognitive dysfunction by triggering beta-amyloid accumulation via the transforming growth factor-beta (TGFbeta)/Smad signaling pathway. PLoS One. 2015;10(10):e0141596. doi:10.1371/journal.pone.0141596.
   PubMed Web of Science ®Google Scholar
• Chen JM, Li QW, Jiang GX, Liu JS, Cheng Q. IL-18 induced IL-23/IL-17 expression impairs Abeta clearance in cultured THP-1 and BV2 cells. Cytokine. 2019;119:113–118. doi:10.1016/j.cyto.2019.03.003.
   PubMed Web of Science ®Google Scholar
• 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 (vol 37, pg 852, 2019). Nat Biotechnol. 2019;37(9):1091. doi:10.1038/s41587-019-0252-6.
   PubMed Web of Science ®Google Scholar
• Lou M, Cao A, Jin C, Mi K, Xiong X, Zeng Z, Pan X, Qie J, Qiu S, Niu Y, et al. Deviated and early unsustainable stunted development of gut microbiota in children with autism spectrum disorder. Gut. pp.gutjnl-2021–325115. 2021. doi:10.1136/gutjnl-2021-325115
   Web of Science ®Google Scholar
• Jing G, Zhang Y, Cui W, Liu L, Xu J, Su X. Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function. BMC Genomics. 2021;22(1):9. doi:10.1186/s12864-020-07307-1.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359. doi:10.1038/nmeth.1923.
   PubMed Web of Science ®Google Scholar
• Nousias O,Montesanto F. Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3. Mar Genomics. 2021;59:100866. doi:10.1016/j.margen.2021.100866.
   PubMed Web of Science ®Google Scholar
• Beghini F, McIver LJ, Blanco-Miguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife. 2021;10. doi:10.7554/eLife.65088
   PubMed Web of Science ®Google Scholar
• Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. doi:10.1093/bioinformatics/btu153.
   PubMed Web of Science ®Google Scholar
• Mershad K, and Said B. DIAMOND: a tool for monitoring the participation of students in online lectures. Educ Inf Technol (Dordr). 2022;27(4):4955–4985. doi:10.1007/s10639-021-10801-y.
   PubMed Web of Science ®Google Scholar
• Drula E, Garron ML, Dogan S, Lombard V, Henrissat B, Terrapon N. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 2022;50(D1):D571–D7. doi:10.1093/nar/gkab1045.
   PubMed Web of Science ®Google Scholar
• Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46(W1):W95–W101. doi:10.1093/nar/gky418.
   PubMed Web of Science ®Google Scholar
• Segata N, Bornigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013;4(1):2304. doi:10.1038/ncomms3304.
   PubMedGoogle Scholar
• Yu GC, Smith DK, Zhu HC, Guan Y, Lam TTY, McInerny G. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8(1):28–36. doi:10.1111/2041-210X.12628.
   Web of Science ®Google Scholar
• Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST server: rapid annotations using subsystems technology. Bmc Genomics. 2008;9(1). doi:10.1186/1471-2164-9-75.
   PubMedGoogle Scholar
• Lin H, and Das Peddada S. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020;11(1):3514. doi:10.1038/s41467-020-17041-7.
   PubMed Web of Science ®Google Scholar
• Friedman J, Alm EJ, von Mering C. Inferring correlation networks from genomic survey data. PLoS Comput Biol. 2012;8(9):e1002687. doi:10.1371/journal.pcbi.1002687.
   PubMed Web of Science ®Google Scholar
• Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, et al. Population-level analysis of gut microbiome variation. Science. 2016;352(6285):560–564. doi:10.1126/science.aad3503.
   PubMed Web of Science ®Google Scholar
• Yin X, Jiang XT, Chai B, Li L, Yang Y, Cole JR, Tiedje JM, Zhang T. ARGs-OAP v2.0 with an expanded SARG database and hidden markov models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics. 2018;34(13):2263–2270. doi:10.1093/bioinformatics/bty053.
   PubMed Web of Science ®Google Scholar
• Guo WG, Rao MB. On optimality of the Benjamini-Hochberg procedure for the false discovery rate. Stat Probab Lett. 2008;78(14):2024–2030. doi:10.1016/j.spl.2008.01.069.
   Web of Science ®Google Scholar