Alterations in the gut virome in patients with ankylosing spondylitis

Abstract

IntroductionAnkylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome.MethodsTo investigate the characteristics of the gut virome in AS, we profiled the gut viral community of 193 AS patients and 59 healthy subjects based on a metagenome-wide analysis of fecal metagenomes from two publicly available datasets.ResultsAS patients revealed a significant decrease in gut viral richness and a considerable alteration of the overall viral structure. At the family level, AS patients had an increased abundance of Gratiaviridae and Quimbyviridae and a decreased abundance of Drexlerviridae and Schitoviridae. We identified 1,004 differentially abundant viral operational taxonomic units (vOTUs) between patients and controls, including a higher proportion of AS-enriched Myoviridae viruses and control-enriched Siphoviridae viruses. Moreover, the AS-enriched vOTUs were more likely to infect bacteria such as Flavonifractor, Achromobacter, and Eggerthellaceae, whereas the control-enriched vOTUs were more likely to be Blautia, Ruminococcus, Collinsella, Prevotella, and Faecalibacterium bacteriophages. Additionally, some viral functional orthologs differed significantly in frequency between the AS-enriched and control-enriched vOTUs, suggesting the functional role of these AS-associated viruses. Moreover, we trained classification models based on gut viral signatures to discriminate AS patients from healthy controls, with an optimal area under the receiver operator characteristic curve (AUC) up to 0.936, suggesting the clinical potential of the gut virome for diagnosing AS.DiscussionThis work provides novel insight into the AS gut virome, and the findings may guide future mechanistic and therapeutic studies for other autoimmune diseases.

Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease

“…Although Streptococcus phages have been reported to be associated with metabolic and autoimmune diseases [ 55 ], their role in IBD has not been reported. In addition, our results showed that IBD-enriched vOTUs were more frequently associated with IBD-related pathogenic bacteria as their hosts, suggesting their involvement in the development of IBD through their prokaryotic hosts, as observed in immune diseases [ 10 , 56 ]. Regarding IBD-depleted viruses, crAss-like and Quimbyviridae are newly identified viral clades that tend to infect Bacteroidetes, which are major polysaccharide degraders in the gut [ 57 ].…”

Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia

“…Only contigs of ≥5 kb in length were used to identify viral sequences in each sample. The identification, decontamination, and dereplication of viral sequences were performed according to the prior studies ( 20 , 47 – 49 ). Briefly, the assembled contigs underwent a stringent quality assessment as follows: (i) contigs were classified as viral if their viral gene content surpassed that of microbial genes, as determined by CheckV v0.7.0 ( 25 ); (ii) contigs exhibiting a P value of less than 0.01 and a score exceeding 0.90 in DeepVirFinder v1.0 ( 50 ); and (iii) identification as viral sequences by VIBRANT v1.2.1 ( 51 ) using default settings.…”

“…Furthermore, gut viral populations constitute significant components of the intestinal microbial ecology and are intimately intertwined with human health. The gut viral homeostasis is carefully maintained under normal conditions; however, it can be disrupted when individuals experience health issues such as inflammatory bowel disease ( 17 ), colorectal cancer ( 18 ), and immune disorders ( 19 – 21 ). Notably, a study has even connected the gut virome of women of childbearing age to polycystic ovary syndrome ( 22 ).…”

Virome in immunodeficiency: what we know currently

“…AS is a chronic autoimmune disease primarily impacting the sacroiliac joints and spine, potentially leading to ankylosis and spinal deformity. [ 67 ] Li et al [ 68 ] examined the gut viral community of 193 AS patients and 59 healthy subjects. Their findings revealed an increase in Myoviridae, crAss-like, and Microviridae in AS patients, while Podoviridae and Siphoviridae decreased compared to the healthy subjects.…”