Khan Mirzaei, M. | bioRxiv Science

bioRxiv2022

Replidec - Use naive Bayes classifier to identify virus lifecycle from metagenomics data

MotivationViruses are the most abundant biological entities on earth. The majority of these entities are bacterial viruses or phages which specifically infect bacteria. Phages can use different replication strategies to invade their hosts including lytic, lysogenic, chronic cycle and pseudolysogeny. While the determination of the replication strategy used by phages is important to explore the phage-bacteria relationships in different ecosystems there are not many tools that can predict this in metagenomic data. In addition, most of the tools available can only predict lytic and lysogenic cycles. To address this issue, we have developed a new software called Replidec to identify three most common phage replication cycles (virulent, temperate, chronic) in viral sequences. ResultsReplidec uses Naive Bayes classifier combined with alignment-based methods to improve the prediction accuracy in metagenomic data. We test Replidec on viral genomes with known replication cycle and simulated metagenomic sequences. Replidec perform relatively good both in isolated genomes (F1 score: 92.29% {+/-} 0.81; mcc: 89.14% {+/-} 1.22) and simulated metagenomic sequences(F1 score: 87.55% {+/-} 2.12; mcc: 88.23% {+/-} 2.55). Moreover, Replidec can also accurately predict the replication cycle in small viral fragments([~]3000bp). In conclusion, Replidec can achieve the best performance in simulated metagenomic data compared to most prediction softwares including BACPHLIP.

bioinformatics↗

bioRxiv2021

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates severity of DSS-colitis

Inflammatory bowel diseases (IBDs) including Crohns disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages) is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown. Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs. Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease.

microbiology↗