Viral metagenomics analysis of feces from coronary heart disease patients reveals the genetic diversity of the <Emphasis Type="Italic">Microviridae</Emphasis>

Recent studies have declared that members of the ssDNA virus family Microviridae play an important role in multiple environments, as they have been found taking a dominant position in the human gut. The aim of this study was to analyze the overall composition of the gut virome in coronary heart disease (CHD) patients, and try to discover the potential link between the human gut virome and CHD. Viral metagenomics methods were performed to detect the viral sequences in fecal samples collected from CHD inpatients and healthy persons as controls. We present the analysis of the virome composition in these CHD patients and controls. Our data shows that the virome composition may be linked to daily living habits and the medical therapy of CHD. Virgaviridae and Microviridae were the two dominant types of viruses found in the enteric virome of CHD patients. Fourteen divergent viruses belonging to the family Microviridae were found, twelve of which were grouped into the subfamily Gokushovirinae, while the remaining two strains might represent two new subfamilies within Microviridae, according to the phylogenetic analysis. In addition, the genomic organization of these viruses has been characterized.

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Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads

Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found in great number among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes highlights the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the microviruses. In addition, a peptidase gene was found in 10 Microviridae and its analysis indicates a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in Microviridae. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.     

Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes

The Microviridae comprises icosahedral lytic viruses with circular single-stranded DNA genomes. The family is divided into two distinct groups based on genome characteristics and virion structure. Viruses infecting enterobacteria belong to the genus Microvirus, whereas those infecting obligate parasitic bacteria, such as Chlamydia, Spiroplasma and Bdellovibrio, are classified into a subfamily, the Gokushovirinae. Recent metagenomic studies suggest that members of the Microviridae might also play an important role in marine environments. In this study we present the identification and characterization of Microviridae-related prophages integrated in the genomes of species of the Bacteroidetes, a phylum not previously known to be associated with microviruses. Searches against metagenomic databases revealed the presence of highly similar sequences in the human gut. This is the first report indicating that viruses of the Microviridae lysogenize their hosts. Absence of associated integrase-coding genes and apparent recombination with dif-like sequences suggests that Bacteroidetes-associated microviruses are likely to rely on the cellular chromosome dimer resolution machinery. Phylogenetic analysis of the putative major capsid proteins places the identified proviruses into a group separate from the previously characterized microviruses and gokushoviruses, suggesting that the genetic diversity and host range of bacteriophages in the family Microviridae is wider than currently appreciated.     

人体肠道病毒组学研究进展

人体微生物组计划开展近10年来,大量的研究显示人体微生物通过各种方式深刻地影响着人体健康。人体肠道内丰富多样的病毒构成了肠道病毒组,是人体微生物组的重要组成部分,和人体健康密切相关。本文综述了近些年国际上人体肠道病毒组研究的最新进展,分别从人体肠道病毒组的组成特征、肠道病毒组-细菌组-人体间的相互作用及其对人体健康的影响、病毒组研究的技术策略及挑战等方面进行了论述,探讨了肠道病毒组在人体疾病预防和治疗领域应用的可行性。     

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin

It is a matter of fact that the human gut microbiome also includes a non‐bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter‐gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre‐agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co‐occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome‐host co‐evolutionary process.     

Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms

There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing the poultry enteric virome have identified novel poultry viruses, but the roles these viruses play in disease and performance problems have yet to be fully characterized. The complex bacterial community present in the poultry gut influences gut development, immune status, and animal health, each of which can be an indicator of overall performance. The present metagenomic investigation was undertaken to provide insight into the colonization of specific pathogen free chickens by enteric microorganisms under field conditions and to compare the pre-contact intestinal microbiome with the altered microbiome following contact with poultry raised in the field. Analysis of the intestinal virome from contact birds (“sentinels”) placed on farms revealed colonization by members of the Picornaviridae, Picobirnaviridae, Reoviridae, and Astroviridae that were not present in pre-contact birds or present in proportionally lower numbers. Analysis of the sentinel gut bacterial community revealed an altered community in the post-contact birds, notably by members of the Lachnospiracea/Clostridium and Lactobacillus families and genera. Members of the avian enteric Reoviridae and Astroviridae have been well-characterized and have historically been implicated in poultry enteric disease; members of the Picobirnaviridae and Picornaviridae have only relatively recently been described in the poultry and avian gut, and their roles in the recognized disease syndromes and in poultry performance in general have not been determined. This metagenomic analysis has provided insight into the colonization of the poultry gut by enteric microbes circulating in commercial broiler flocks, and has identified enteric viruses and virus communities that warrant further study in order to understand their role(s) in avian gut health and disease.     

Assessing the diversity and specificity of two freshwater viral communities through metagenomics

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.     

Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing

The human respiratory tract is heavily exposed to microorganisms. Viral respiratory tract pathogens, like RSV, influenza and rhinoviruses cause major morbidity and mortality from respiratory tract disease. Furthermore, as viruses have limited means of transmission, viruses that cause pathogenicity in other tissues may be transmitted through the respiratory tract. It is therefore important to chart the human virome in this compartment. We have studied nasopharyngeal aspirate samples submitted to the Karolinska University Laboratory, Stockholm, Sweden from March 2004 to May 2005 for diagnosis of respiratory tract infections. We have used a metagenomic sequencing strategy to characterize viruses, as this provides the most unbiased view of the samples. Virus enrichment followed by 454 sequencing resulted in totally 703,790 reads and 110,931 of these were found to be of viral origin by using an automated classification pipeline. The snapshot of the respiratory tract virome of these 210 patients revealed 39 species and many more strains of viruses. Most of the viral sequences were classified into one of three major families; Paramyxoviridae, Picornaviridae or Orthomyxoviridae. The study also identified one novel type of Rhinovirus C, and identified a number of previously undescribed viral genetic fragments of unknown origin.     

病毒组研究：微生物组研究新热点

病毒组是指分布在各种环境中病毒的集合或病毒宏基因组的统称。病毒可以分布于水体、冰川、动植物甚至某些病毒当中,主要分为真核病毒、原核病毒和亚病毒。其在维持环境内稳态、生态系统平衡等方面起着非常重要的作用,并且与人类的健康密切相关。近年来,随着测序技术和数据分析水平的进步,人们能够采用宏基因组测序的方式研究病毒组并探究其在生态位中的潜在作用。人们在冰川、海洋、各种动植物中都得到了大量的病毒组数据,发现了众多未知病毒。人们研究病毒组主要是通过宏基因组数据挖掘和病毒样粒子 (Virus-like particles,VLPs) 分离富集测序两种方式进行分析处理。迄今为止,已存在多种不同的病毒组分离富集方法,并且针对病毒组的生物信息分析也数不胜数。然而,针对病毒组的富集和数据分析方法还缺少具体、完整的综述。文中将对病毒组的分离富集方法和数据分析进行整理与总结,并列举出部分采用病毒组分离富集方法进行的重要研究,旨在为相关人员提供参考,进一步促进病毒组研究领域的发展。     

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease

The gut microbiota plays a crucial role in coronary heart disease (CHD). However, only a few studies focusing on the relationship between gut microbiota and CHD in ethnic populations are available. Here, we employed shotgun sequencing of the gut metagenome to analyze the taxonomic composition and functional annotation of the gut microbiota of 14 CHD patients, 13 patients with non-stenosis coronary heart disease (NCHD), and 18 healthy controls (HT) in Tibetan subjects. We found that the α-diversity of the gut microbiota was not significantly different among the three groups., whereas β-diversity was significantly altered in the CHD group compared with HT. Based on the receiver operating characteristic curve (ROC) analysis, the relative abundance of Proteobacteria species effectively distinguished patients with CHD from the control group. Most of the enriched species belonged to Proteobacteria. The pathways that contributed the most to the differences between groups were amino acid metabolism-related pathways, especially lysine biosynthesis. The enzymes of the lysine biosynthesis pathway, including K01714 and K00821, were significantly decreased in the CHD group. Our findings increase the understanding of the association between CHD pathogenesis and gut microbiota in the Tibetan population, thus paving the way for the development of improved diagnostic methods and treatments for Tibetan patients with CHD.     

Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater

Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource.     

Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa

Next-generation sequencing (NGS) has the potential to transform the discovery of viruses causing unexplained acute febrile illness (UAFI) because it does not depend on culturing the pathogen or a priori knowledge of the pathogen’s nucleic acid sequence. More generally, it has the potential to elucidate the complete human virome, including viruses that cause no overt symptoms of disease, but may have unrecognized immunological or developmental consequences. We have used NGS to identify RNA viruses in the blood of 195 patients with UAFI and compared them with those found in 328 apparently healthy (i.e., no overt signs of illness) control individuals, all from communities in southeastern Nigeria. Among UAFI patients, we identified the presence of nucleic acids from several well-characterized pathogenic viruses, such as HIV-1, hepatitis, and Lassa virus. In our cohort of healthy individuals, however, we detected the nucleic acids of two novel rhabdoviruses. These viruses, which we call Ekpoma virus-1 (EKV-1) and Ekpoma virus-2 (EKV-2), are highly divergent, with little identity to each other or other known viruses. The most closely related rhabdoviruses are members of the genus Tibrovirus and Bas-Congo virus (BASV), which was recently identified in an individual with symptoms resembling hemorrhagic fever. Furthermore, by conducting a serosurvey of our study cohort, we find evidence for remarkably high exposure rates to the identified rhabdoviruses. The recent discoveries of novel rhabdoviruses by multiple research groups suggest that human infection with rhabdoviruses might be common. While the prevalence and clinical significance of these viruses are currently unknown, these viruses could have previously unrecognized impacts on human health; further research to understand the immunological and developmental impact of these viruses should be explored. More generally, the identification of similar novel viruses in individuals with and without overt symptoms of disease highlights the need for a broader understanding of the human virome as efforts for viral detection and discovery advance.     

Viral metagenomics reveals diverse viruses in the fecal samples of children with diarrhea

Diarrhea is the third leading cause of death in developing countries in children under the age of five. About half a million children die of diarrhea every year, most of which in developing countries. Viruses are the main pathogen of diarrhea. In China, the fecal virome of children with diarrhea has been rarely studied. Using an unbiased viral metagenomics approach, we analyzed the fecal virome in children with diarrhea. Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae, Astroviridae, Caliciviridae, Parvoviridae, Picornaviridae, and Reoviridae. Among them, the family of Caliciviridae accounts for the largest proportion of 78.42%, following with Adenoviridae (8.94%) and Picornaviridae (8.36%). In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea, the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus. This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.     

The fecal viral flora of California sea lions

California sea lions are one of the major marine mammal species along the Pacific coast of North America. Sea lions are susceptible to a wide variety of viruses, some of which can be transmitted to or from terrestrial mammals. Using an unbiased viral metagenomic approach, we surveyed the fecal virome in California sea lions of different ages and health statuses. Averages of 1.6 and 2.5 distinct mammalian viral species were shed by pups and juvenile sea lions, respectively. Previously undescribed mammalian viruses from four RNA virus families (Astroviridae, Picornaviridae, Caliciviridae, and Reoviridae) and one DNA virus family (Parvoviridae) were characterized. The first complete or partial genomes of sapeloviruses, sapoviruses, noroviruses, and bocavirus in marine mammals are reported. Astroviruses and bocaviruses showed the highest prevalence and abundance in California sea lion feces. The diversity of bacteriophages was higher in unweaned sea lion pups than in juveniles and animals in rehabilitation, where the phage community consisted largely of phages related to the family Microviridae. This study increases our understanding of the viral diversity in marine mammals, highlights the high rate of enteric viral infections in these highly social carnivores, and may be used as a baseline viral survey for comparison with samples from California sea lions during unexplained disease outbreaks.     

The secret garden's gardeners

The role of the microbial fauna in our gut for health and well-being is undisputed. Now, scientists are discovering that gut viruses also play a crucial role in modulating our risk for a wide range of diseases.Research has shown that the microbiota—the population of micro-organisms inhabiting the gut—has a profound influence on health in both humans and animals. However, most studies have largely ignored the viral population of the gut—the virome—although it is much larger, both in number of organisms and in genetic diversity. This is because the virome was thought to be less important for health and immunity, as it mainly comprises bacteriophages that only affect bacteria. However, researchers are beginning to realize that the viruses present might well be important in human health, as they manipulate the microbiota, swapping genetic virulence factors among bacteria, and through interaction with the host immune system.There are two distinct categories of virus in the gut: phages, which infect bacteria, and viruses that target host cells. Although these two categories are apparently independent of each other, there is a relationship between them, as indicated by growing evidence that the microbiota as a whole, including phages, has a crucial role in protecting against bacterial and viral infections [1].The phage and bacteria populations of the gut have an intricate relationship, which raises the potential therapeutic use of phages to treat a variety of conditions caused by bacteria in the gut, especially those involving chronic inflammation. The first step, however, is to explore and analyse the phage populations in the gut in terms of diversity and number, along with their interactions with their bacterial targets. This has proven to be a major challenge, given the enormous difficulties in identifying, isolating and amplifying genetic material from the phage population.Nevertheless, researchers from the Weizmann Institute of Science and Tel Aviv University in Israel have made substantial progress by indirectly identifying phages through clustered regularly interspaced short palindromic repeats (CRISPRs) in their bacterial hosts [2]. CRISPRs function as a prokaryotic adaptive immune system against genetic invaders such as phages by recognizing foreign DNA and then silencing its expression in a manner analogous to RNA interference (RNAi) in eukaryotes. Short segments of the foreign DNA, known as spacers, are incorporated into the bacterial genome to provide the memory of past exposures to enable recognition of phage DNA.The phage and bacteria populations of the gut have an intricate relationship, which raises the potential therapeutic use of phages to treat a variety of conditions…The Israeli study reconstructed the CRISPR bacterial immune system in the human gut microbiomes of 124 European individuals, and from that identified 991 phages targeted in at least one of the individuals. Of these phages, 78% were present in at least two individuals and some turned out to be the same ones that had already been identified in Japanese and American people. This global distribution of particular phages was a surprise, given that in other ecological niches, notably seawater, where phages are highly abundant, there is great genetic diversity among the populations, even over short distances.The Israeli team further succeeded in deducing the bacterial hosts of 130 of the phages, which allowed them to study the associated phage–bacteria interactions. It turned out that a subset of the phages had developed closer associations with their host bacteria as lysogenized prophages after fusing their DNA with the bacterial chromo-some or as plasmids. Rotem Sorek, a specialist in microbial warfare at the Weizmann Institute of Science and co-author of the Israel study, commented that this behaviour allows bacteria to take advantage of the phage by incorporating and transmitting genes that provide vital functions and occasionally aid pathogenesis. “There are clear instances of phages ‘helping'' pathogenic bacteria to attack humans,” Sorek said. “The toxins of the Cholera, Diphtheria and Shigella (disenteria) are all carried by phages that are integrated into the bacterial genome.”Horizontal gene transfer among bacteria has long been known to increase the adaptability of several potentially virulent bacterial species, but it is only recently that the mechanisms involving prophages have begun to be elucidated. A significant advance was made in a Japanese study from the University of Miyazaki, inspired by the observation that many sequenced bacterial genomes contain multiple prophages carrying a wide range of genes involved in virulence, and that these often seem to contain genetic defects [3]. The team analysed a virulent strain of Escherichia coli, known as O157, which contains 18 prophages that encode various genes involved in the production of virulence factors, including two potent cytotoxins: Shiga toxins 1 and 2. Most of the prophages they identified contained multiple genetic defects, yet they seemed to be capable of transporting virulence elements between not only members of the same strain but also different E. coli strains.The conclusion from their study was that defective prophages in close proximity within E. coli cells were still capable of recombining to yield a new phage that was released from the cell and could infect other cells nearby in the gut. It seems that these defective prophages were not just evolutionary leftovers, but were important components of the bacterial genome, conferring additional adaptive flexibility through horizontal gene transfer. Many other bacteria contain multiple prophages with genetic defects, so it is probable that this mechanism is not confined to E. coli.Other studies have focused on the composition of phage virus populations outside bacteria in the gut, as part of initiatives to compare and contrast the virome and bacteriome in response to individual genetic variation and environmental factors such as diet. One might imagine that phage and bacteria populations should be closely correlated, but it turns out that there are significant differences in the level of variation between individuals, as well as over time within the same individual. A study at the Washington University School of Medicine, USA, on monozygotic twins, found that in contrast to bacteriomes, viromes tended to be unique to individuals and less varied over time in response to changes in diet or other factors. By contrast, the bacterial population changed much more with diet and was also quite similar between twins.“There are clear instances of phages ‘helping'' pathogenic bacteria to attack humans”…Given that there is a direct relationship between the bacteria of the gut and the immune system of the individual—which is not the case for phage viruses—these findings make a degree of sense. Furthermore, as noted by Jeffrey Gordon, co-author of the Washington University study, there is not a one-to-one relationship between bacteria and the phages they host: “It''s been shown in other environments that you can have several different viruses capable of infecting the same bacterial host, while the specificity of each virus is usually quite narrow, typically extending only to a few strains within a species-level phylotype,” he explained. “This leads to a greater genetic diversity in the virome. Furthermore, a viral genome is enriched for genes involved in genome replication and virion assembly. Thus, the functional composition of the virome and the microbiome are quite different.”The situation is different for non-phage viruses in the gut that have a direct relationship with the human or animal host. The main research interest here is the three-way relationship between the virus, the bacteriome and the host''s immune system. Research on this front has already led to a new understanding of the role played by the entire microbiome in immunity. Often, the microbiome provides protection against viruses, but in some cases it can encourage their propagation. This is relevant in the context of human immunodeficiency virus (HIV), for example, given that the virus infects immune cells such as helper T cells, macrophages and dendritic cells, the activity and production of which in turn are related to the microbiota. An important question is whether the course of HIV and its possible development into symptomatic acquired immunodeficiency syndrome (AIDS) might be encouraged by the microbiota, if it stimulates production of such immune cells. Whilst this has yet to be established for AIDS, there is evidence that it is the case in monkeys carrying the related simian immunodeficiency virus (SIV), which infects at least 45 species of African primates. Unlike HIV in humans, SIV is usually non-pathogenic, as many primates evolved to coexist with the virus; but it does cause AIDS in rhesus macaque monkeys.Another Washington University School of Medicine study, this time looking at the link between viruses, the bacteriome and host immunity, began with the insight that animals developing AIDS experience immune hyperactivation, including higher levels of inflammatory chemokines, cytokines and activated T cells. This observation suggested that excessive inflammation is an important factor in progression to AIDS, presumably because it increases the number of cells vulnerable to HIV and SIV infection. The US team investigated whether there were any corresponding changes in the virome, finding that whilst it remains unchanged in uninfected animals, including rhesus macaque monkeys that had not succumbed to AIDS, its diversity increases significantly in infected macaques with full-blown AIDS [4].Often, the microbiome provides protection against viruses, but in some cases it can encourage their propagationThe team is following up by probing the relationship between enteric viruses and AIDS and how the immune system is stimulated. The animals suffer from progressive damage to their intestinal walls, which could increase the absorption of viruses that in turn stimulate the immune system, promoting replication of SIV and possibly encouraging more opportunistic viral infection, thereby creating a vicious circle. “This is one of several possible scenarios that we are actively investigating,” commented Scott Handley, lead author of the study. “What is uncertain is what is causing the damage to the intestinal wall. It could be the viruses which expand in the enteric virome during SIV infection, or some other factor, which could be immune-mediated or some other microbe or microbial product in the enteric microbiome.”Handley''s team has identified some of the viruses involved, including both common ones and some previously undiscovered. “Many of the viruses we identified have been associated with [gastrointestinal] disease in one form or another,” Handley said. “It is true that many of the viruses we identified are common; however, we identified at least 32 novel subtypes of these viruses never seen before.” He added that it remains to be established whether SIV infection encourages opportunistic infection by these viruses or not: “We don''t really have a good handle on what viruses would be considered ‘commensal'' viruses in any animal, including research primates. So whether they are already there when infection with SIV occurs, or are just more susceptible to opportunistic infection, is unclear.”Handley further commented that this work could lead to new therapeutic targets for treating HIV infection and preventing AIDS, and he is investigating whether the same expansion of the enteric virome occurs in humans infected with HIV. “In addition, we are interested to see if vaccination can reverse the enteric virome expansion,” he explained. “We would also like to better understand if the viruses we have identified were already circulating in these primates, or are succumbing to opportunistic infections.”Handley argued that his team''s work and that of others provides a compelling case for devoting more resources to studying the role of viruses in the gut, which would require further advances in laboratory and analytical techniques. “One challenge with studying the viral members of a microbiome is that there are no well-defined marker sequences,” he said. “Therefore, we are largely dependent on random shotgun sequencing approaches, which are less efficient and more expensive. Not only do you have to gather much more data, the computational analysis required is much more complex than the well-established techniques developed for studying the bacterial microbiome. While we know there is a great deal of interest in studying the virome, current techniques and technology tend to limit the number of labs that can participate in these efforts. We are very interested in developing new tools and techniques to help alleviate this issue.”An important question is whether the course of HIV […] might be encouraged by the microbiota, if it stimulates production of such immune cellsWork undertaken so far has already shown that probiotic or prebiotic treatments that provide or encourage beneficial gut bacteria can benefit patients infected with HIV. Improvements in intestinal health could reduce the leakage of all antigens, including viral ones, through the intestinal wall. More generally, a better understanding of how phages, viruses and bacteria in the gut interact could lead to new therapies that manipulate the microbiome to restore intestinal health in sufferers of a variety of conditions, including those involving chronic inflammation.     

Association between living environment and human oral viral ecology

The human oral cavity has an indigenous microbiota known to include a robust community of viruses. Very little is known about how oral viruses are spread throughout the environment or to which viruses individuals are exposed. We sought to determine whether shared living environment is associated with the composition of human oral viral communities by examining the saliva of 21 human subjects; 11 subjects from different households and 10 unrelated subjects comprising 4 separate households. Although there were many viral homologues shared among all subjects studied, there were significant patterns of shared homologues in three of the four households that suggest shared living environment affects viral community composition. We also examined CRISPR (clustered regularly interspaced short palindromic repeat) loci, which are involved in acquired bacterial and archaeal resistance against invading viruses by acquiring short viral sequences. We analyzed 2 065 246 CRISPR spacers from 5 separate repeat motifs found in oral bacterial species of Gemella, Veillonella, Leptotrichia and Streptococcus to determine whether individuals from shared living environments may have been exposed to similar viruses. A significant proportion of CRISPR spacers were shared within subjects from the same households, suggesting either shared ancestry of their oral microbiota or similar viral exposures. Many CRISPR spacers matched virome sequences from different subjects, but no pattern specific to any household was found. Our data on viromes and CRISPR content indicate that shared living environment may have a significant role in determining the ecology of human oral viruses.     

中国部分地区蝙蝠携带病毒的宏基因组学分析

蝙蝠携带有60多种病毒,其中许多对人有高度致病性.为了解中国蝙蝠携带病毒的自然本底、蝙蝠病毒的多样性和挖掘潜在的病毒病原,通过基于Solexa高通量测序的病毒宏基因组学技术对从吉林、云南、湖南采集的蝙蝠组织进行病毒组学研究,获得了11 644 232条读长(Reads),并拼接出44 872条重叠序列(Contig).通过核酸序列注释发现,其中8.2％(4 002/44 872)的重叠序列与病毒相关,能进一步注释到36个病毒科,包括19种脊椎动物病毒、6种植物病毒、4种昆虫病毒和4种噬菌体.通过对重叠序列的遗传进化分析、多序列比对显示,被注释为细小病毒、腺联病毒、博卡病毒、腺病毒、小双节RNA病毒等的重叠序列与已知病毒相似,部分序列却又呈现出明显的序列差异.通过对腺病毒和博卡病毒进一步的PCR扩增证实了此研究方法可靠.旨在了解我国蝙蝠携带病毒组的构成,对建立高效的野生动物源人兽共患病的监测方法提供参考.     

Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans

Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn''s disease, ulcerative colitis and colorectal cancer (CRC). We used 454 titanium pyrosequencing of the V1–V2 region of the 16S rRNA gene to characterize adherent bacterial communities in mucosal biopsy samples from 33 subjects with adenomas and 38 subjects without adenomas (controls). Biopsy samples from subjects with adenomas had greater numbers of bacteria from 87 taxa than controls; only 5 taxa were more abundant in control samples. The magnitude of the differences in the distal gut microbiota between patients with adenomas and controls was more pronounced than that of any other clinical parameters including obesity, diet or family history of CRC. This suggests that sequence analysis of the microbiota could be used to identify patients at risk for developing adenomas.