{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T10:50:04Z","timestamp":1788000604598,"version":"build-2784847793"},"reference-count":112,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,10,20]],"date-time":"2023-10-20T00:00:00Z","timestamp":1697760000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Degenerative Cervical Myelopathy (DCM) is the most common cause of spinal cord impairment in elderly populations. It describes a spectrum of disorders that cause progressive spinal cord compression, neurological impairment, loss of bladder and bowel functions, and gastrointestinal dysfunction. The gut microbiota has been recognized as an environmental factor that can modulate both the function of the central nervous system and the immune response through the microbiota-gut-brain axis. Changes in gut microbiota composition or microbiota-producing factors have been linked to the progression and development of several pathologies. However, little is known about the potential role of the gut microbiota in the pathobiology of DCM. Here, DCM was induced in C57BL\/6 mice by implanting an aromatic polyether material underneath the C5-6 laminae. The extent of DCM-induced changes in microbiota composition was assessed by 16S rRNA sequencing of the fecal samples. The immune cell composition was assessed using flow cytometry. To date, several bacterial members have been identified using BLAST against the largest collection of metagenome-derived genomes from the mouse gut. In both, female and males DCM caused gut dysbiosis compared to the sham group. However, dysbiosis was more pronounced in males than in females, and several bacterial members of the families Lachnospiraceae and Muribaculaceae were significantly altered in the DCM group. These changes were also associated with altered microbe-derived metabolic changes in propionate-, butyrate-, and lactate-producing bacterial members. Our results demonstrate that DCM causes dynamic changes over time in the gut microbiota, reducing the abundance of butyrate-producing bacteria, and lactate-producing bacteria to a lesser extent. Genome-scale metabolic modeling using gapseq successfully identified pyruvate-to-butanoate and pyruvate-to-propionate reactions involving genes such as Buk and ACH1, respectively. These results provide a better understanding of the sex-specific molecular effects of changes in the gut microbiota on DCM pathobiology.<\/jats:p>","DOI":"10.3389\/fmicb.2023.1229783","type":"journal-article","created":{"date-parts":[[2023,10,20]],"date-time":"2023-10-20T13:19:40Z","timestamp":1697807980000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":6,"title":["Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice"],"prefix":"10.3389","volume":"14","author":[{"given":"Carlos","family":"Farkas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"Retamal-Fredes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ariel","family":"\u00c1vila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael G.","family":"Fehlings","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pia M.","family":"Vidal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,10,20]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1087","DOI":"10.1126\/science.abi6087","article-title":"Signaling inflammation across the gut-brain axis","volume":"374","author":"Agirman","year":"2021","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1093\/bioinformatics\/btz859","article-title":"KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold","volume":"36","author":"Aramaki","year":"2020","journal-title":"Bioinformatics"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous clostridium species","volume":"331","author":"Atarashi","year":"2011","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1038\/s41582-019-0303-0","article-title":"Degenerative cervical myelopathy - update and future directions","volume":"16","author":"Badhiwala","year":"2020","journal-title":"Nat. Rev. Neurol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"eabf1861","DOI":"10.1126\/sciimmunol.abf1861","article-title":"Microbial uptake in oral mucosa-draining lymph nodes leads to rapid release of cytotoxic CD8(+) T cells lacking a gut-homing phenotype","volume":"7","author":"Barreto de Alburquerque","year":"2022","journal-title":"Sci. Immunol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1016\/S1474-4422(20)30454-3","article-title":"A new dimension in degenerative cervical myelopathy","volume":"20","author":"Bartels","year":"2021","journal-title":"Lancet Neurol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e1005544","DOI":"10.1371\/journal.pcbi.1005544","article-title":"BacArena: individual-based metabolic modeling of heterogeneous microbes in complex communities","volume":"13","author":"Bauer","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"12743","DOI":"10.1038\/s41598-021-92027-z","article-title":"Changes in gut microbiota in the acute phase after spinal cord injury correlate with severity of the lesion","volume":"11","author":"Bazzocchi","year":"2021","journal-title":"Sci. Rep."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/s41467-020-20422-7","article-title":"Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma","volume":"12","author":"Behary","year":"2021","journal-title":"Nat. Commun."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"10719","DOI":"10.1073\/pnas.1711233114","article-title":"Gut microbiota from multiple sclerosis patients enables spontaneous autoimmune encephalomyelitis in mice","volume":"114","author":"Berer","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1093\/brain\/awv375","article-title":"Spinal cord injury-induced immune deficiency syndrome enhances infection susceptibility dependent on lesion level","volume":"139","author":"Brommer","year":"2016","journal-title":"Brain"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"eabn1823","DOI":"10.1126\/sciadv.abn1823","article-title":"Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis","volume":"8","author":"Bronge","year":"2022","journal-title":"Sci. Adv."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1016\/j.molmed.2012.06.003","article-title":"Pathogenic features of CD4+CD28- T cells in immune disorders","volume":"18","author":"Broux","year":"2012","journal-title":"Trends Mol. Med."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","article-title":"Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms","volume":"6","author":"Caporaso","year":"2012","journal-title":"ISME J."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.bbi.2022.06.002","article-title":"Sex, pain, and the microbiome: the relationship between baseline gut microbiota composition, gender and somatic pain in healthy individuals","volume":"104","author":"Caputi","year":"2022","journal-title":"Brain Behav. Immun."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"D471","DOI":"10.1093\/nar\/gkv1164","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases","volume":"44","author":"Caspi","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1177\/2192568220953811","article-title":"Outcomes of degenerative cervical myelopathy from the perspective of persons living with the condition: findings of a Semistructured interview process with partnered internet survey","volume":"12","author":"Davies","year":"2022","journal-title":"Glob. Spine J."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"e149227","DOI":"10.1172\/jci.insight.149227","article-title":"The influence of ApoE4 on the clinical outcomes and pathophysiology of degenerative cervical myelopathy","volume":"6","author":"Desimone","year":"2021","journal-title":"JCI Insight"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1111\/j.1365-2958.2010.07381.x","article-title":"Vitamin B6 biosynthesis is essential for survival and virulence of Mycobacterium tuberculosis","volume":"78","author":"Dick","year":"2010","journal-title":"Mol. Microbiol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1038\/s42255-022-00670-1","article-title":"Genome-microbiome interplay provides insight into the determinants of the human blood metabolome","volume":"4","author":"Diener","year":"2022","journal-title":"Nat. Metab."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"2589","DOI":"10.1093\/bioinformatics\/btv209","article-title":"edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test","volume":"31","author":"Dimont","year":"2015","journal-title":"Bioinformatics"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"e01356-20","DOI":"10.1128\/mSystems.01356-20","article-title":"Spinal cord injury changes the structure and functional potential of gut bacterial and viral communities","volume":"6","author":"du","year":"2021","journal-title":"mSystems"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1079\/BJN20041150","article-title":"Contribution of acetate to butyrate formation by human faecal bacteria","volume":"91","author":"Duncan","year":"2004","journal-title":"Br. J. Nutr."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2187","DOI":"10.1128\/JB.00041-13","article-title":"The vitamin B(6) biosynthesis pathway in Streptococcus pneumoniae is controlled by pyridoxal 5\u2032-phosphate and the transcription factor PdxR and has an impact on ear infection","volume":"195","author":"el Qaidi","year":"2013","journal-title":"J. Bacteriol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"e0121216","DOI":"10.1371\/journal.pone.0121216","article-title":"A complete pathway model for lipid a biosynthesis in Escherichia coli","volume":"10","author":"Emiola","year":"2014","journal-title":"PLoS One"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"e1319","DOI":"10.7717\/peerj.1319","article-title":"Anvi'o: an advanced analysis and visualization platform for 'omics data","volume":"3","author":"Eren","year":"2015","journal-title":"PeerJ"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"2260","DOI":"10.1016\/j.cmet.2021.10.010","article-title":"Microbiota-derived acetate enables the metabolic fitness of the brain innate immune system during health and disease","volume":"33","author":"Erny","year":"2021","journal-title":"Cell Metab."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"e00051-17","DOI":"10.1128\/mSystems.00051-17","article-title":"Insights into butyrate production in a controlled fermentation system via gene predictions","volume":"2","author":"Esquivel-Elizondo","year":"2017","journal-title":"mSystems"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1038\/nature12721","article-title":"Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells","volume":"504","author":"Furusawa","year":"2013","journal-title":"Nature"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"11450","DOI":"10.1038\/s41598-017-11734-8","article-title":"Butyrate-producing bacteria supplemented in vitro to Crohn's disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity","volume":"7","author":"Geirnaert","year":"2017","journal-title":"Sci. Rep."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e0145878","DOI":"10.1371\/journal.pone.0145878","article-title":"Intestinal microbiota in patients with spinal cord injury","volume":"11","author":"Gungor","year":"2016","journal-title":"PLoS One"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/978-1-4939-8728-3_8","article-title":"16S rRNA gene analysis with QIIME2","volume":"1849","author":"Hall","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"Harris","year":"2020","journal-title":"Nature"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"977","DOI":"10.1038\/nbt.1672","article-title":"High-throughput generation, optimization and analysis of genome-scale metabolic models","volume":"28","author":"Henry","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"113009","DOI":"10.1016\/j.expneurol.2019.113009","article-title":"Gastrointestinal dysfunction after spinal cord injury","volume":"320","author":"Holmes","year":"2019","journal-title":"Exp. Neurol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"100815","DOI":"10.1016\/j.yfrne.2019.100815","article-title":"You've got male: sex and the microbiota-gut-brain axis across the lifespan","volume":"56","author":"Jaggar","year":"2020","journal-title":"Front. Neuroendocrinol."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1186\/s40168-021-01007-y","article-title":"Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis","volume":"9","author":"Jing","year":"2021","journal-title":"Microbiome"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gky962","article-title":"New approach for understanding genome variations in KEGG","volume":"47","author":"Kanehisa","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1007\/978-1-59745-251-9_3","article-title":"Multiple alignment of DNA sequences with MAFFT","volume":"537","author":"Katoh","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"e1009947","DOI":"10.1371\/journal.pcbi.1009947","article-title":"Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart","volume":"18","author":"Kieser","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"2603","DOI":"10.1084\/jem.20151345","article-title":"Gut dysbiosis impairs recovery after spinal cord injury","volume":"213","author":"Kigerl","year":"2016","journal-title":"J. Exp. Med."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"fcaa234","DOI":"10.1093\/braincomms\/fcaa234","article-title":"Mir21 modulates inflammation and sensorimotor deficits in cervical myelopathy: data from humans and animal models","volume":"3","author":"Laliberte","year":"2021","journal-title":"Brain Commun."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"3626","DOI":"10.3390\/jcm10163626","article-title":"Degenerative cervical myelopathy: clinical presentation, assessment, and natural history","volume":"10","author":"Lannon","year":"2021","journal-title":"J. Clin. Med."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1038\/nature10434","article-title":"Peripheral education of the immune system by colonic commensal microbiota","volume":"478","author":"Lathrop","year":"2011","journal-title":"Nature"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"eabp9960","DOI":"10.1126\/science.abp9960","article-title":"The microbiome and gut homeostasis","volume":"377","author":"Lee","year":"2022","journal-title":"Science"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"2909","DOI":"10.1016\/j.celrep.2020.02.036","article-title":"An integrated metagenome Catalog reveals new insights into the murine gut microbiome","volume":"30","author":"Lesker","year":"2020","journal-title":"Cell Rep."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1111\/1462-2920.13589","article-title":"Formation of propionate and butyrate by the human colonic microbiota","volume":"19","author":"Louis","year":"2017","journal-title":"Environ. Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1007\/s10753-019-01133-8","article-title":"The anti-inflammatory immune regulation induced by butyrate is impaired in inflamed intestinal mucosa from patients with ulcerative colitis","volume":"43","author":"Magnusson","year":"2020","journal-title":"Inflammation"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"43859","DOI":"10.1038\/srep43859","article-title":"Microbiota alteration is associated with the development of stress-induced despair behavior","volume":"7","author":"Marin","year":"2017","journal-title":"Sci. Rep."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"e68626","DOI":"10.1371\/journal.pone.0068626","article-title":"Effects of sodium butyrate and its synthetic amide derivative on liver inflammation and glucose tolerance in an animal model of steatosis induced by high fat diet","volume":"8","author":"Mattace Raso","year":"2013","journal-title":"PLoS One"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1146\/annurev-med-042320-014032","article-title":"The gut-brain Axis","volume":"73","author":"Mayer","year":"2022","journal-title":"Annu. Rev. Med."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1093\/gbe\/evu050","article-title":"A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria","volume":"6","author":"Meehan","year":"2014","journal-title":"Genome Biol. Evol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1038\/nri3738","article-title":"Regional specialization within the intestinal immune system","volume":"14","author":"Mowat","year":"2014","journal-title":"Nat. Rev. Immunol."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"19535","DOI":"10.1074\/jbc.M500612200","article-title":"Biosynthesis of UDP-N-acetyl-L-fucosamine, a precursor to the biosynthesis of lipopolysaccharide in Pseudomonas aeruginosa serotype O11","volume":"280","author":"Mulrooney","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"107999","DOI":"10.1016\/j.isci.2023.107999","article-title":"Intestinal microbial circadian rhythms drive sex differences in host immunity and metabolism","volume":"26","author":"Munyoki","year":"2023","journal-title":"iScience"},{"key":"ref68","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1038\/s41586-023-06431-8","article-title":"Mapping the T cell repertoire to a complex gut bacterial community","volume":"621","author":"Nagashima","year":"2023","journal-title":"Nature"},{"key":"ref69","doi-asserted-by":"publisher","first-page":"624","DOI":"10.3390\/jcm9030624","article-title":"The relationship between gastrointestinal comorbidities, clinical presentation and surgical outcome in patients with DCM: analysis of a global cohort","volume":"9","author":"Nouri","year":"2020","journal-title":"J. Clin. Med."},{"key":"ref70","doi-asserted-by":"publisher","first-page":"39S","DOI":"10.1177\/21925682211036071","article-title":"Degenerative cervical myelopathy: development and natural history [AO spine RECODE-DCM research priority number 2]","volume":"12","author":"Nouri","year":"2022","journal-title":"Glob. Spine J."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"2159","DOI":"10.1089\/neu.2017.5349","article-title":"Investigation of microbiota alterations and intestinal inflammation post-spinal cord injury in rat model","volume":"35","author":"O'Connor","year":"2018","journal-title":"J. Neurotrauma"},{"key":"ref72","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"277","DOI":"10.3389\/fimmu.2019.00277","article-title":"Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases","volume":"10","author":"Parada Venegas","year":"2019","journal-title":"Front. Immunol."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.3390\/nu14102078","article-title":"Dietary vitamin B1 intake influences gut microbial community and the consequent production of short-chain fatty acids","volume":"14","author":"Park","year":"2022","journal-title":"Nutrients"},{"key":"ref75","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/mi.2014.44","article-title":"Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR-S6K pathway","volume":"8","author":"Park","year":"2015","journal-title":"Mucosal Immunol."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"2389","DOI":"10.1111\/1462-2920.12350","article-title":"Improved group-specific primers based on the full SILVA 16S rRNA gene reference database","volume":"16","author":"Pfeiffer","year":"2014","journal-title":"Environ. Microbiol."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1186\/1471-2105-11-45","article-title":"NeatMap--non-clustering heat map alternatives in R","volume":"11","author":"Rajaram","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"185","DOI":"10.3389\/fmicb.2016.00185","article-title":"Intestinal short chain fatty acids and their link with diet and human health","volume":"7","author":"R\u00edos-Covi\u00e1n","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1016\/j.cell.2016.11.018","article-title":"Gut microbiota regulate motor deficits and Neuroinflammation in a model of Parkinson's disease","volume":"167","author":"Sampson","year":"2016","journal-title":"Cells"},{"key":"ref82","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1038\/s41586-018-0595-z","article-title":"Cervical excitatory neurons sustain breathing after spinal cord injury","volume":"562","author":"Satkunendrarajah","year":"2018","journal-title":"Nature"},{"key":"ref83","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"ref84","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH image to ImageJ: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"ref85","doi-asserted-by":"publisher","first-page":"e1002533","DOI":"10.1371\/journal.pbio.1002533","article-title":"Revised estimates for the number of human and bacteria cells in the body","volume":"14","author":"Sender","year":"2016","journal-title":"PLoS Biol."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/s41586-022-04884-x","article-title":"The gut metabolite indole-3 propionate promotes nerve regeneration and repair","volume":"607","author":"Serger","year":"2022","journal-title":"Nature"},{"key":"ref87","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1186\/s13059-020-02195-w","article-title":"Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome","volume":"21","author":"Shaiber","year":"2020","journal-title":"Genome Biol."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"ref89","doi-asserted-by":"publisher","first-page":"258","DOI":"10.3389\/fmicb.2019.00258","article-title":"Differential view on the bile acid stress response of Clostridioides difficile","volume":"10","author":"Sievers","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"7428","DOI":"10.1523\/JNEUROSCI.1114-16.2016","article-title":"Microbiota dysbiosis controls the neuroinflammatory response after stroke","volume":"36","author":"Singh","year":"2016","journal-title":"J. Neurosci."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1080\/10790268.2020.1762829","article-title":"Epidemiology of non-traumatic spinal cord injury in Ireland - a prospective population-based study","volume":"45","author":"Smith","year":"2022","journal-title":"J. Spinal Cord Med."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1126\/science.1241165","article-title":"The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis","volume":"341","author":"Smith","year":"2013","journal-title":"Science"},{"key":"ref93","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1128\/mBio.00886-20","article-title":"Vitamin biosynthesis by human gut butyrate-producing bacteria and cross-feeding in synthetic microbial communities","volume":"11","author":"Soto-Martin","year":"2020","journal-title":"mBio"},{"key":"ref94","doi-asserted-by":"publisher","first-page":"550420","DOI":"10.3389\/fmicb.2020.550420","article-title":"Interpretations of environmental microbial community studies are biased by the selected 16S rRNA (gene) amplicon sequencing pipeline","volume":"11","author":"Straub","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"878382","DOI":"10.3389\/fnut.2022.878382","article-title":"Your regulatory T cells are what you eat: how diet and gut microbiota affect regulatory T cell development","volume":"9","author":"Tan","year":"2022","journal-title":"Front. Nutr."},{"key":"ref96","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1093\/nar\/28.1.33","article-title":"The COG database: a tool for genome-scale analysis of protein functions and evolution","volume":"28","author":"Tatusov","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref97","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1038\/nn.4289","article-title":"Silencing spinal interneurons inhibits immune suppressive autonomic reflexes caused by spinal cord injury","volume":"19","author":"Ueno","year":"2016","journal-title":"Nat. Neurosci."},{"key":"ref98","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1038\/s41385-020-00354-7","article-title":"Dopaminergic signalling limits suppressive activity and gut homing of regulatory T cells upon intestinal inflammation","volume":"14","author":"Ugalde","year":"2021","journal-title":"Mucosal Immunol."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"11496","DOI":"10.3390\/ijms231911496","article-title":"Acute systemic white blood cell changes following degenerative cervical myelopathy (DCM) in a mouse model","volume":"23","author":"Ulndreaj","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"ref100","doi-asserted-by":"publisher","first-page":"e0241285","DOI":"10.1371\/journal.pone.0241285","article-title":"Effects of experimental cervical spinal cord injury on peripheral adaptive immunity","volume":"15","author":"Ulndreaj","year":"2020","journal-title":"PLoS One"},{"key":"ref101","doi-asserted-by":"publisher","first-page":"1209","DOI":"10.1089\/neu.2016.4498","article-title":"Characterization of the antibody response after cervical spinal cord injury","volume":"34","author":"Ulndreaj","year":"2016","journal-title":"J. Neurotrauma"},{"key":"ref102","doi-asserted-by":"publisher","first-page":"e92512","DOI":"10.1172\/jci.insight.92512","article-title":"Delayed decompression exacerbates ischemia-reperfusion injury in cervical compressive myelopathy","volume":"2","author":"Vidal","year":"2017","journal-title":"JCI Insight"},{"key":"ref103","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1186\/s12974-018-1257-7","article-title":"Methylprednisolone treatment enhances early recovery following surgical decompression for degenerative cervical myelopathy without compromise to the systemic immune system","volume":"15","author":"Vidal","year":"2018","journal-title":"J. Neuroinflammation"},{"key":"ref104","doi-asserted-by":"publisher","first-page":"577024","DOI":"10.1016\/j.jneuroim.2019.577024","article-title":"The changes in systemic monocytes in humans undergoing surgical decompression for degenerative cervical myelopathy may influence clinical neurological recovery","volume":"336","author":"Vidal","year":"2019","journal-title":"J. Neuroimmunol."},{"key":"ref105","doi-asserted-by":"publisher","first-page":"4793","DOI":"10.1073\/pnas.0900408106","article-title":"Identification of IL-17-producing FOXP3+ regulatory T cells in humans","volume":"106","author":"Voo","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref106","doi-asserted-by":"publisher","first-page":"6733","DOI":"10.1038\/s41467-022-34526-9","article-title":"T cell responses at diagnosis of amyotrophic lateral sclerosis predict disease progression","volume":"13","author":"Yazdani","year":"2022","journal-title":"Nat. Commun."},{"key":"ref107","doi-asserted-by":"publisher","first-page":"1277","DOI":"10.1093\/brain\/awr054","article-title":"Human neuropathological and animal model evidence supporting a role for Fas-mediated apoptosis and inflammation in cervical spondylotic myelopathy","volume":"134","author":"Yu","year":"2011","journal-title":"Brain"},{"key":"ref108","doi-asserted-by":"publisher","first-page":"27572","DOI":"10.1038\/srep27572","article-title":"Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium","volume":"6","author":"Zhang","year":"2016","journal-title":"Sci. Rep."},{"key":"ref109","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1186\/s12967-018-1735-9","article-title":"Gut microbiota dysbiosis in male patients with chronic traumatic complete spinal cord injury","volume":"16","author":"Zhang","year":"2018","journal-title":"J. Transl. Med."},{"key":"ref110","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1186\/s12876-016-0500-x","article-title":"Butyrate inhibits interleukin-17 and generates Tregs to ameliorate colorectal colitis in rats","volume":"16","author":"Zhang","year":"2016","journal-title":"BMC Gastroenterol."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"111681","DOI":"10.1016\/j.celrep.2022.111681","article-title":"Commensal cow Roseburia reduces gut-dysbiosis-induced mastitis through inhibiting bacterial translocation by producing butyrate in mice","volume":"41","author":"Zhao","year":"2022","journal-title":"Cell Rep."},{"key":"ref112","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/s13059-021-02295-1","article-title":"Gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models","volume":"22","author":"Zimmermann","year":"2021","journal-title":"Genome Biol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1229783\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,20]],"date-time":"2023-10-20T13:19:45Z","timestamp":1697807985000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1229783\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,20]]},"references-count":112,"alternative-id":["10.3389\/fmicb.2023.1229783"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2023.1229783","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,20]]},"article-number":"1229783"}}