Gut microbiome differences between amyotrophic lateral sclerosis patients and spouse controls

References

• Wu S, Yi J, Zhang Y, Zhou J, Sun J. Leaky intestine and impaired microbiome in an amyotrophic lateral sclerosis mouse model. Physiol Rep. 2015;3:e12356.
   PubMed Web of Science ®Google Scholar
• Zhang YG, Wu S, Yi J, Xia Y, Jin D, Zhou J, et al. Target intestinal microbiota to alleviate disease progression in amyotrophic lateral sclerosis. Clin Ther. 2017;39:322–36.
   PubMed Web of Science ®Google Scholar
• Burberry A, Wells MF, Limone F, Couto A, Smith KS, Keaney J, et al. C9orf72 suppresses systemic and neural inflammation induced by gut bacteria. Nature 2020;582:89–94.
   PubMed Web of Science ®Google Scholar
• Fang X, Wang X, Yang S, Meng F, Wang X, Wei H, et al. Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing. Front Microbiol. 2016;7:1479.
   PubMed Web of Science ®Google Scholar
• Rowin J, Xia Y, Jung B, Sun J. Gut inflammation and dysbiosis in human motor neuron disease. Physiol Rep. 2017;5:e13443.
   PubMed Web of Science ®Google Scholar
• Nicholson K, Bjornevik K, Abu-Ali G, Chan J, Cortese M, Dedi B, et al. The human gut microbiota in people with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener. 2020.
   PubMed Web of Science ®Google Scholar
• Brenner D, Hiergeist A, Adis C, Mayer B, Gessner A, Ludolph AC, et al. The fecal microbiome of ALS patients. Neurobiol Aging. 2018;61:132–7.
   PubMed Web of Science ®Google Scholar
• Mazzini L, Mogna L, De FM, Amoruso A, Pane M, Aloisio I, et al. Potential role of gut microbiota in ALS pathogenesis and possible novel therapeutic strategies. J Clin Gastroenterol. 2018;52:S68–S70.
   PubMed Web of Science ®Google Scholar
• Blacher E, Bashiardes S, Shapiro H, Rothschild D, Mor U, Dori-Bachash M, et al. Potential roles of gut microbiome and metabolites in modulating ALS in mice. Nature. 2019;572:474–80.
   PubMed Web of Science ®Google Scholar
• Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, et al. Transmission of human-associated microbiota along family and social networks. Nat Microbiol. 2019;4:964–71.
   PubMed Web of Science ®Google Scholar
• Dill-McFarland KA, Tang ZZ, Kemis JH, Kerby RL, Chen G, Palloni A, et al. Close social relationships correlate with human gut microbiota composition. Sci Rep. 2019;9:703.
   PubMed Web of Science ®Google Scholar
• Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018;555:210–5.
   PubMed Web of Science ®Google Scholar
• Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, et al. Cohabiting family members share microbiota with one another and with their dogs. Elife. 2013;2:e00458.
   PubMed Web of Science ®Google Scholar
• Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79:5112–20.
   PubMed Web of Science ®Google Scholar
• Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
   PubMed Web of Science ®Google Scholar
• Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
   PubMed Web of Science ®Google Scholar
• Edgar R. UCHIME2: improved chimera prediction for amplicon sequencing. bioRxiv. 2016:074252.
   Google Scholar
• Edgar RC. Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics. 2018;34:2371–5.
   PubMed Web of Science ®Google Scholar
• Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
   PubMed Web of Science ®Google Scholar
• Love M, Anders S, Huber W. Differential analysis of count data–the DESeq2 package. Genome Biol. 2014;15:10.1186.
   Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
   PubMed Web of Science ®Google Scholar
• R Core Team. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing; 2017.
   Google Scholar
• Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. 2004;20:289–90.
   PubMed Web of Science ®Google Scholar
• Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package. Community Ecology Package. 2007;10:631–7.
   Google Scholar
• Cule E, Vineis P, De Iorio M. Significance testing in ridge regression for genetic data. BMC Bioinformatics. 2011;12:372.
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol. 1995;57:289–300.
   Web of Science ®Google Scholar
• Aßhauer KP, Wemheuer B, Daniel R, Meinicke P. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics. 2015;31:2882–4.
   PubMed Web of Science ®Google Scholar
• Carroll IM, Ringel-Kulka T, Keku TO, Chang YH, Packey CD, Sartor RB, et al. Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome. Am J Physiol Gastrointest Liver Physiol. 2011;301:G799–807.
   PubMed Web of Science ®Google Scholar
• Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM, et al. Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol. 2015;67:128–39.
   PubMed Web of Science ®Google Scholar
• Wacklin P, Kaukinen K, Tuovinen E, Collin P, Lindfors K, Partanen J, et al. The duodenal microbiota composition of adult celiac disease patients is associated with the clinical manifestation of the disease. Inflamm Bowel Dis. 2013;19:934–41.
   PubMed Web of Science ®Google Scholar
• Wang M, Karlsson C, Olsson C, Adlerberth I, Wold AE, Strachan DP, Martricardi PM, et al. Reduced diversity in the early fecal microbiota of infants with atopic eczema. J Allergy Clin Immunol. 2008;121:129–34.
   PubMed Web of Science ®Google Scholar
• Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–11.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature. 2009;457:480–4.
   PubMed Web of Science ®Google Scholar
• Bailey MT, Dowd SE, Galley JD, Hufnagle AR, Allen RG, Lyte M. Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressor-induced immunomodulation. Brain Behav Immun. 2011;25:397–407.
   PubMed Web of Science ®Google Scholar
• Knowles SR, Nelson EA, Palombo EA. Investigating the role of perceived stress on bacterial flora activity and salivary cortisol secretion: a possible mechanism underlying susceptibility to illness. Biol Psychol. 2008;77:132–7.
   PubMed Web of Science ®Google Scholar
• O'Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM, Quigley EM, et al. Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biol Psychiatry. 2009;65:263–7.
   PubMed Web of Science ®Google Scholar
• Hill-Burns E, Debelius J, Morton J, Wissemann W, Lewis M, Wallen Z, et al. Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome. Mov Disord. 2017;32:739–49.
   PubMed Web of Science ®Google Scholar
• Houser MC, Chang J, Factor SA, Molho ES, Zabetian CP, Hill‐Burns EM, et al. Stool immune profiles evince gastrointestinal inflammation in Parkinson’s disease. Mov Disord. 2018;33:793–804.
   PubMed Web of Science ®Google Scholar
• Hasegawa S, Goto S, Tsuji H, Okuno T, Asahara T, Nomoto K, et al. Intestinal dysbiosis and lowered serum lipopolysaccharide-binding protein in Parkinson’s Disease. PLoS One. 2015;10:e0142164.
   PubMed Web of Science ®Google Scholar
• Keshavarzian A, Green SJ, Engen PA, Voigt RM, Naqib A, Forsyth CB, et al. Colonic bacterial composition in Parkinson’s disease. Mov Disord. 2015;30:1351–60.
   PubMed Web of Science ®Google Scholar
• Sampson T, Debelius J, Thron T, Janssen S, Shastri G, Ilhan Z, et al. Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson’s Disease. Cell. 2016;167:1469–80.
   PubMed Web of Science ®Google Scholar
• Scheperjans F, Aho V, Pereira PA, Koskinen K, Paulin L, Pekkonen E, et al. Gut microbiota are related to Parkinson’s disease and clinical phenotype. Mov Disord. 2015;30:350–8.
   PubMed Web of Science ®Google Scholar
• Unger MM, Spiegel J, Dillmann KU, Grundmann D, Philippeit H, Bürmann J, et al. Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls. Parkinsonism Relat Disord. 2016;32:66–72.
   PubMed Web of Science ®Google Scholar
• Bedarf J, Hildebrand F, Coelho L, Sunagawa S, Bahram M, Goeser F, et al. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients. Genome Med. 2017;9:39.
   PubMed Web of Science ®Google Scholar
• Hopfner F, Künstner A, Müller SH, Künzel S, Zeuner KE, Margraf NG, et al. Gut microbiota in Parkinson disease in a northern German cohort. Brain Res. 2017;1667:41–5.
   PubMed Web of Science ®Google Scholar
• Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, et al. Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Sci Rep. 2016;6:28484.
   PubMed Web of Science ®Google Scholar
• Cosorich I, Dalla-Costa G, Sorini C, Ferrarese R, Messina MJ, Dolpady J, et al. High frequency of intestinal TH17 cells correlates with microbiota alterations and disease activity in multiple sclerosis. Sci Adv. 2017;3:e1700492.
   PubMed Web of Science ®Google Scholar
• Jangi S, Gandhi R, Cox LM, Li N, von Glehn FAO, Yan R, et al. Alterations of the human gut microbiome in multiple sclerosis. Nat Commun. 2016;7:12015.
   PubMed Web of Science ®Google Scholar
• Miyake S, Kim S, Suda W, Oshima K, Nakamura M, Matsuoka T, et al. Dysbiosis in the gut microbiota of patients with multiple aclerosis, with a striking depletion of species belonging to Clostridia XIVa and IV clusters. PLoS Biol. 2015;10:e0137429.
   Google Scholar
• Cekanaviciute E, Yoo BB, Runia TF, Debelius JW, Singh S, Nelson CA, et al. Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. Proc Natl Acad Sci USA. 2017;114:10713–8.
   PubMed Web of Science ®Google Scholar
• De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, et al. Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013;8:e76993.
   PubMed Web of Science ®Google Scholar
• Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe. 2010;16:444–53.
   PubMed Web of Science ®Google Scholar
• Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334:105–8.
   PubMed Web of Science ®Google Scholar
• van Teijlingen NH, Helgers LC, Zijlstra-Willems EM, van Hamme JL, Ribeiro CM, Strijbis K, et al. Vaginal dysbiosis associated-bacteria Megasphaera elsdenii and Prevotella timonensis induce immune activation via dendritic cells. J Reprod Immunol. 2020;138:103085.
   PubMed Web of Science ®Google Scholar