Gut virome:New key players in the pathogenesis of inflammatory bowel disease

Inflammatory bowel disease(IBD)is a chronic inflammatory illness of the intes-tine.While the mechanism underlying the pathogenesis of IBD is not fully under-stood,it is believed that a complex combination of host immunological response,environmental exposure,particularly the gut microbiota,and genetic suscept-ibility represents the major determinants.The gut virome is a group of viruses found in great frequency in the gastrointestinal tract of humans.The gut virome varies greatly among individuals and is influenced by factors including lifestyle,diet,health and disease conditions,geography,and urbanization.The majority of research has focused on the significance of gut bacteria in the progression of IBD,although viral populations represent an important component of the microbiome.We conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.

Increased fecal viral content associated with obesity in mice

AIM: To investigate the presence of total gut viral content in obese mice, and establish correlation with obesity associated metabolic measures and gut microbiome.METHODS: Fresh fecal samples were collected from normal and obese(Leptin deficient Lep^(ob/ob)) mice. Total viral DNA and RNA was isolated and quantified for establishing the correlation with metabolic measures and composition of gut bacterial communities.RESULTS: In this report, we found that obese mice feces have higher viral contents in terms of total viral DNA and RNA(P < 0.001). Interestingly, these increased viral DNA and RNA content were tightly correlated with metabolic measures, i.e., body weight, fat mass and fasting blood glucose. Total viral content were positively correlated with firmicutes(R^2 > 0.6), whilst negatively correlated with bacteroidetes and bifidobacteria. CONCLUSION: This study suggests the strong correlation of increased viral population into the gut of obese mice and opens new avenues to explore the role of gut virome in pathophysiology of obesity.

Torque teno virus in liver diseases: On the way towards unity of view

The review presents the data accumulated for more than 20 years of research of torque teno virus(TTV).Its molecular genetic structure,immunobiology,epidemiology,diagnostic methods,possible replication sites,and pathogenicity factors are described.TTV is a virus that is frequently detectable in patients with different viral hepatitides,in cases of hepatitis without an obvious viral agent,as well as in a healthy population.There is evidence suggesting that biochemical and histological changes occur in liver tissue and bile duct epithelium in TTV monoinfection.There are sufficient histological signs of liver damage,which confirm that the virus can undergo a replicative cycle in hepatocytes.Along with this,cytological hybridization in TTV-infected cells has shown no substantial cytopathic(cell-damaging)effects that are characteristic of pathogenic hepatotropic viruses.Studying TTV has led to the evolution of views on its role in the development of human pathology.The first ideas about the hepatotropism of the virus were gradually reformed as new data became available on the prevalence of the virus and its co-infection with other viruses,including the viruses of the known types of hepatitides.The high prevalence of TTV in the human population indicates its persistence in the body as a virome and a nonpathogenic virus.It has recently been proposed that the level of TTV DNA in the blood of patients undergoing organ transplantation should be used as an endogenous marker of the body’s immune status.The available data show the polytropism of the virus and deny the fact that TTV can be assigned exclusively to hepatitis viruses.Fortunately,the rare detection of the damaging effect of TTV on hepatic and bile duct epithelial cells may be indirect evidence of its conditionally pathogenic properties.The ubiquity of the virus and the variability of its existence in humans cannot put an end to its study.

Metagenomic analysis reveals presence of different animal viruses in commercial fetal bovine serum and trypsin

Animal-derived biological products, such as fetal bovine serum(FBS) and trypsin, are important supplements for scientific, pharmaceutical, and medical use. Although preventive guidelines and tests are implemented to reduce potential viral contamination in these biologicals, they do not target unusual or emerging viruses, leading to safety concerns. Using unbiased metagenomics, we investigated the presence of viruses in recently collected commercial FBS and trypsin samples from different geographic regions. In total, we detected viralsequencesbelongingto Parvoviridae,Anelloviridae,Flaviviridae,Herpesviridae,Caliciviridae, Nodaviridae, Rhabdoviridae, and Paramyxoviridae, including several viruses related to bovine diseases, viruses of potential human and insect origin, and viruses of unknown origin. Bovine parvovirus 3 and bosavirus were detected with high frequency and abundance in FBS, necessitating more stringent testing for these parvoviruses during production. Both bovine norovirus and bovine viral diarrhea virus 1 displayed relatively high genetic distance to closest hits, indicating the presence of new genotypes in farm animals. While the origin of novel lyssavirus and Nipah virus is unclear, their presence raises the possibility of the introduction of pathogenic animal-derived viruses into biologicals.Our results showed relatively widespread contamination of different viruses in biologicals,underscoring the need for robust safety protocol alternatives, such as metagenomic sequencing, to monitor emerging viruses.

Intestinal virome:An important research direction for alcoholic and nonalcoholic liver diseases

In recent years,the interaction between the gut microflora and liver diseases has attracted much attention.The intestinal microflora is composed of bacteria,archaea,fungi and viruses.There are few studies on the intestinal virome,and whether it has a causal relationship with bacterial changes in the gut is still unclear.However,it is undeniable that the intestinal virome is also a very important portion of the blueprint for the development of liver diseases and the diagnosis and therapeutic modalities in the future.

Virome in healthy pangolins reveals compatibility with multiple potentially zoonotic viruses

Previous studies have identified multiple viruses in dead or severely diseased pangolins,but descriptions of the virome in healthy pangolins are lacking.This poses a greater risk of cross-species transmission due to poor preventive awareness and frequent interactions with breeders.In this study,we investigated the viral composition of 34 pangolins with no signs of disease at the time of sampling and characterized a large number of arthropodassociated viruses belonging to 11 families and vertebrate viruses belonging to eight families,including those with pathogenic potential in humans and animals.Several important vertebrate viruses were identified in the pangolins,including parvovirus,pestivirus,and picobirnavirus.The picobirnavirus was clustered with human and grey teal picobirnaviruses.Viruses with cross-species transmission ability were also identified,including circovirus,rotavirus,and astrovirus.Our study revealed that pangolins are frequently exposed to arthropod-associated viruses in the wild and can carry many vertebrate viruses under natural conditions.This study provides important insights into the virome of pangolins,underscoring the importance of monitoring potential pathogens in healthy pangolins to prevent outbreaks of infectious diseases in domesticated animals and humans.

Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China

Objective To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake,China.Methods Ten smear samples were collected in March 2019.Metagenomic sequencing was performed to delineate bacterial and viral diversity.Taxonomic analysis was performed using the Kraken2 and Bracken methods.A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase(RdRp)region of picornavirus.Results We identified 363 bacterial and 6 viral families.A significant difference in microbial and viral abundance was found between samples S01–S09 and S10.In S01–S09,members of Flavobacteriia and Gammaproteobacteria were the most prevalent,while in S10,the most prevalent bacteria class was Actinomycetia.Among S01–S09,members of Myoviridae and Herelleviridae were the most prevalent,while the dominant virus family of S10 was Picornaviridae.The full genome of the pigeon mesivirus-like virus(NC-BM-233)was recovered from S10 and contained an open reading frame of 8,124 nt.It showed the best hit to the pigeon mesivirus 2 polyprotein,with 84.10%amino acid identity.Phylogenetic analysis showed that RdRp clustered into Megrivirus B.Conclusion This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples,broadens our knowledge of viral and bacterial diversity,and is a way to discover potential pathogens in wild birds .

Human pegivirus infection after transplant:Is there an impact?

The microbiome's role in transplantation has received growing interest,but the role of virome remains understudied.Pegiviruses are single-stranded positivesense RNA viruses,historically associated with liver disease,but their pathogenicity is controversial.In the transplantation setting,pegivirus infection does not seem to have a negative impact on the outcomes of solid-organ and hematopoietic stem cell transplant recipients.However,the role of pegiviruses as proxies in immunosuppression monitoring brings novelty to the field of virome research in immunocompromised individuals.The possible immunomodulatory effect of pegivirus infections remains to be elucidated in further trials.

Viromes of Haemaphysalis longicornis reveal different viral abundance and diversity in free and engorged ticks

Haemaphysalis longicornis ticks,commonly found in East Asia,can transmit various pathogenic viruses,includingthe severe fever with thrombocytopenia syndrome virus(SFTSV)that has caused febrile diseases among humansin Hubei Province.However,understanding of the viromes of H.longicornis was limited,and the prevalence ofviruses among H.longicornis ticks in Hubei was not well clarified.This study investigates the viromes of bothengorged(fed)and free(unfed)H.longicornis ticks across three mountainous regions in Hubei Province from 2019to 2020.RNA-sequencing analysis identified viral sequences that were related to 39 reference viruses belonging tounclassified viruses and seven RNA viral families,namely Chuviridae,Nairoviridae,Orthomyxoviridae,Parvoviridae,Phenuiviridae,Rhabdoviridae,and Totiviridae.Viral abundance and diversity in these ticks were analysed,andphylogenetic characteristics of the Henan tick virus(HNTV),Dabieshan tick virus(DBSTV),Okutama tick virus(OKTV),and Jingmen tick virus(JMTV)were elucidated based on their full genomic sequences.Prevalenceanalysis demonstrated that DBSTV was the most common virus found in individual H.longicornis ticks(12.59%),followed by HNTV(0.35%),whereas JMTV and OKTV were not detected.These results improve our understanding of H.longicornis tick viromes in central China and highlight the role of tick feeding status and geographyin shaping the viral community.The findings of new viral strains and their potential impact on public health raisethe need to strengthen surveillance efforts for comprehensively assessing their spillover potentials.

RNA viromes of Dermacentor nuttalli ticks reveal a novel uukuvirus in Qinghai Province,China

Ticks are a major parasite on the Qinghai-Tibet Plateau,western China,and represent an economic burden to agriculture and animal husbandry.Despite research on tick-borne pathogens that threaten humans and animals,the viromes of dominant tick species in this area remain unknown.In this study,we collected Dermacentor nuttalli ticks near Qinghai Lake and identified 13 viruses belonging to at least six families through metagenomic sequencing.Four viruses were of high abundance in pools,including Xınjiang tick-associated virus 1(XJTAV1),and three novel viruses:Qinghai Lake virus 1,Qinghai Lake virus 2(QHLV1,and QHLV2,unclassified),and Qinghai Lake virus 3(QHLV3,genus Uukuvirus of family Phenuiviridae in order Bunyavirales),which lacks the M segment.The minimum infection rates of the four viruses in the tick groups were 8.2%,49.5%,6.2%,and 24.7%,respectively,suggesting the prevalence of these viruses in D.nuttalli ticks.A putative M segment of QHLV3 was identified from the next-generation sequencing data and further characterized for its signal peptide cleavage site,N-glycosylation,and transmembrane region.Furthermore,we probed the L,M,and S segments of other viruses from sequencing data of other tick pools by using the putative M segment sequence of QHLV3.By revealing the viromes of D.nuttalli ticks,this study enhances our understanding of tick-borne viral communities in highland regions.The putative M segment identified in a novel uukuvirus suggests that previously identified uukuviruses without M segments should have had the same genome organization as typical bunyaviruses.These findings will facilitate virus discovery and our understanding of the phylogeny of tick-borne uukuviruses.

Soil microbial ecology through the lens of metatranscriptomics

Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental conditions.The double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional metatranscriptomics.By contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA depletion.In this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics.In particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and viromes.Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.

The multi-kingdom microbiome catalog of the chicken gastrointestinal tract

Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs.Despite recent significant advances in gut microbiome studies,a comprehensive study of chicken gut bacterial,archaeal,and viral genomes remains unavailable.In this study,we constructed a chicken multi-kingdom microbiome catalog(CMKMC),including 18,201 bacterial,225 archaeal,and 33,411 viral genomes,and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes(MAGs)from ten countries.We found that 812 and 240 MAGs in our dataset were putative novel species and genera,respectively,far beyond what was previously reported.The newly unclassified MAGs were predominant in Phyla Firmicutes_A(n=263),followed by Firmicutes(n=126),Bacteroidota(n=121),and Proteobacteria(n=87).Most of the classified species-level viral oper-ational taxonomic units belong to Caudovirales.Approximately,63.24%of chicken gut viromes are predicted to infect two or more hosts,including complete circular viruses.Moreover,we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses.Together,our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date,functional insights into the chicken gastrointestinal tract microbiota,and paves the way for microbial interventions for better chicken health and productivity.

Another piece of puzzle for the human microbiome: the gut virome under dietary modulation

The virome is the most abundant and highly variable microbial consortium in the gut.Because of difficulties in isolating and culturing gut viruses and the lack of reference genomes,the virome has remained a rela-tively elusive aspect of the human microbiome.In recent years,studies on the virome have accumulated growing evidence showing that the virome is diet-modulated and widely involved in regulating health.Here,we review the responses of the gut virome to dietary intake and the potential health implications,presenting changes in the gut viral community and preferences of viral members to particular diets.We further discuss how viral-bacterial interactions and phage lifestyle shifts shape the gut microbiota.We also discuss the specific functions conferred by diet on the gut virome and bacterial community in the context of horizontal gene transfer,as well as the import of new viral members along with the diet.Collating these studies will expand our understanding of the dietary regulation of the gut virome and inspire dietary in-terventions and health maintenance strategies targeting the gut microbiota.

PHISDetector:A Tool to Detect Diverse In Silico Phage–host Interaction Signals for Virome Studies

Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe interactions leave diverse signals in bacterial and phage genomic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interaction signals.In the present study,we developed a novel tool phage-host interaction signal detector(PHISDetector)to predict phage-host interactions by detecting and integrating diverse in silico PHISs,and scoring the probability of phage-host interactions using machine learning models based on PHIS features.We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases.When tested on a dataset of 758 annotated phage-host pairs,PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels,respectively,outperforming other phage-host prediction tools.When applied to 125,842 metagenomic viral contigs(mVCs)derived from 3042 geographically diverse samples,a detection rate of 54.54% could be achieved.Furthermore,PHISDetector could predict infecting phages for 85.6% of 368 multidrug-resistant(MDR)bacteria and 30% of 454 human gut bacteria obtained from the National Institutes of Health(NIH)Human Microbiome Project(HMP).The PHISDetector can be run either as a web server(http://www.microbiome-bigdata.com/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://github.com/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.

Prediction of the Receptorome for the Human-Infecting Virome

The virus receptors are key for the viral infection of host cells.Identification of the virus receptors is still challenging at present.Our previous study has shown that human virus receptor proteins have some unique features including high N-glycosylation level,high number of interaction partners and high expression level.Here,a random-forest model was built to identify human virus receptorome from human cell membrane proteins with an accepted accuracy based on the combination of the unique features of human virus receptors and protein sequences.A total of 1424 human cell membrane proteins were predicted to constitute the receptorome of the human-infecting virome.In addition,the combination of the random-forest model with protein–protein interactions between human and viruses predicted in previous studies enabled further prediction of the receptors for 693 human-infecting viruses,such as the enterovirus,norovirus and West Nile virus.Finally,the candidate alternative receptors of the SARS-Co V-2 were also predicted in this study.As far as we know,this study is the first attempt to predict the receptorome for the human-infecting virome and would greatly facilitate the identification of the receptors for viruses.

Viromes in marine ecosystems reveal remarkable invertebrate RNA virus diversity

Little is known about ocean viromes and the ecological drivers of the evolution of aquatic RNA viruses.This study employed a meta-transcriptomic approach to characterize the viromes of 58 marine invertebrate species across three seas.This revealed the presence of 315 newly identified RNA viruses in nine viral families or orders(Durnavirales,Totiviridae,Bunyavirales,Han-taviridae,Picornavirales,Flaviviridae,Hepelivirales,Solemoviridae,and Tombusviridae),with most of them being sufficiently divergent to the already documented viruses.Notably,this study revealed three marine invertebrate hantaviruses that are rooted to vertebrate hantaviruses,further supporting that hantaviruses may have a marine origin.We have also found evidence for possible host sharing and switch events during virus evolution.Overall,we have revealed the hidden diversity of marine invertebrate RNA viruses.

Comparison of Viromes in Ticks from Different Domestic Animals in China

Ticks are involved in the transmission of various arboviruses and some tick-borne viruses pose significant threats to the health of humans or livestock.This study aimed to investigate the geographical distribution of tick species and tickassociated viruses in central and eastern China.Total 573 ticks from domestic animals including dogs,sheep and cattle were collected in 2017.Two genera of ticks were identified including Rhipicephalus and Haemaphysalis.Sequencing was performed on Miseq Illumina platform to characterize the tick viromes from the four different sampling locations.Following trimming,13,640 reads were obtained and annotated to 19 virus families.From these sequences,above 37.74%of the viral reads were related to the RNA viruses.Virome comparison study revealed that the tick viral diversity was considerably different in the two identified tick genera.The viral diversity of R.microplus was significantly different from that of other Rhipicephalus species.On the other hand,substantial overlap in viral species was observed between the same genera.In addition,we found no evidence that the natural host played a major role in shaping virus diversity based on the comparison of their viromes.Rather,the geographic location seems to significantly influence the viral families.Phylogenetic study indicated that the novel negative-sense RNA viruses identified in this study was closely related to Bole tick virus 1 and 3 viruses.In conclusion,the present study provides a baseline for comparing viruses detected in ticks,according to species,natural hosts,and geographic locations.

Disturbed gut virome with potent interferonogenic property in systemic lupus erythematosus

Accumulating evidence suggests an essential role of disturbed gut microbiota in the etiopathogenesis of systemic lupus erythematosus(SLE),but it remains unclear as to gut virome.In this study,fecal virus-like particles(VLPs)isolated from 76 non-treated SLE patients and 75 healthy controls were subjected to gut virome profiling.The proportion of bacteriophages was significantly elevated in the SLE gut,and the altered viral taxa were correlated with clinical parameters.Gut virome and bacteriome were closely associated with each other in SLE patients.The combination of gut viral and bacterial markers displayed better performance in distinguishing SLE patients from healthy controls.Further,VLPs from non-treated SLE patients promoted interferon-a production in an epithelial cell line and human immune cells.Intriguingly,the interferon-stimulatory capacity diminished in VLPs from post-treated SLE patients.Our findings may shed novel insights into SLE pathogenesis.Further in-depth understanding of gut virome might help develop future biomarkers and therapeutics for SLE patients.

Virome diversity of ticks feeding on domestic mammals in China

Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses.From 2017 to 2018,640 ticks were collected in eight different provinces in central and western China.Six species were detected,including H.longicornis,De.everestianus,Rh.microplus,Rh.turanicus,Rh.sanguineous,and Hy.asiaticum.Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform,resulting in 13.44 G(5.88×10^(7))of 250-bp-end reads,in which 2,437,941 are viral reads.We found 27 nearly complete genome sequences,including 16 genome sequences encoding entire protein-coding regions(lack of 30 or 50 end non-coding regions)and complete viral genomes,distributed in the arboviral family(Chuviridae,Rhabdoviridae,Nairoviridae,Phenuiviridae,Flaviviridae,Iflaviridae)as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans.In addition,13 virus sequences found in Chuviridae,Nairoviridae,Flaviviridae,Iflaviridae,Hepeviridae,Parvoviridae,and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera.Besides,an epidemiological survey shows a high prevalence(9.38%and 15.63%)of two viruses(Ovine Copiparvovirus and Bovine parvovirus 2)in the tick cohort.

Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan,a tropical island of China

The risk of emerging infectious diseases(EID)is increasing globally.More than 60%of EIDs worldwide are caused by animal-borne pathogens.This study aimed to characterize the virome,analyze the phylogenetic evolution,and determine the diversity of rodent-borne viruses in Hainan Province,China.We collected 682 anal and throat samples from rodents,combined them into 28 pools according to their species and location,and processed them for next-generation sequencing and bioinformatics analysis.The diverse viral contigs closely related to mammals were assigned to 22 viral families.Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as arenavirus,coronavirus,astrovirus,pestivirus,parvovirus,and papillomavirus.We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling,and bocavirus in Rattus andamanensis from the national nature reserves of Bangxi with low amino acid identity to known pathogens are proposed as the novel species,and their rodent hosts have not been previously reported to carry these viruses.These results expand our knowledge of viral classification and host range and suggest that there are highly diverse,undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas.