AIM:To study whether selected bacterial 16S ribosomal RNA(rRNA)gene phylotypes are capable of disting- uishing irritable bowel syndrome(IBS). METHODS:The faecal microbiota of twenty volunteers with IBS,subdivided into...AIM:To study whether selected bacterial 16S ribosomal RNA(rRNA)gene phylotypes are capable of disting- uishing irritable bowel syndrome(IBS). METHODS:The faecal microbiota of twenty volunteers with IBS,subdivided into eight diarrhoea-predominant (IBS-D),eight constipation-predominant(IBS-C)and four mixed symptom-subtype(IBS-M)IBS patients,and fifteen control subjects,were analysed at three time-points with a set of fourteen quantitative real-timepolymerase chain reaction assays.All assays targeted 16S rRNA gene phylotypes putatively associated with IBS,based on 16S rRNA gene library sequence analysis. The target phylotypes were affiliated with Actinobac-teria,Bacteroidetes and Firmicutes.Eight of the target phylotypes had less than 95%similarity to cultured bacterial species according to their 16S rRNA gene sequence.The data analyses were made with repeated-measures ANCOVA-type modelling of the data and principle component analysis(PCA)with linear mixed-effects models applied to the principal component scores. RESULTS:Bacterial phylotypes Clostridium cocleatum 88%,Clostridium thermosuccinogenes 85%,Coprobacillus catenaformis 91%,Ruminococcus bromii-like, Ruminococcus torques 91%,and R.torques 93%were detected from all samples analysed.A multivariate analysis of the relative quantities of all 14 bacterial 16S rRNA gene phylotypes suggested that the intestinal microbiota of the IBS-D patients differed from other sample groups.The PCA on the first principal component(PC1),explaining 30.36%of the observed variation in the IBS-D patient group,was significantly altered from all other sample groups(IBS-D vs control, P=0.01;IBS-D vs IBS-M,P=0.00;IBS-D vs IBS-C, P=0.05).Significant differences were also observed in the levels of distinct phylotypes using relative values in proportion to the total amount of bacteria.A phy- lotype with 85%similarity to C.thermosuccinogenes was quantified in significantly different quantities among the IBS-D and control subjects(-4.08±0.90 vs -3.33±1.16,P=0.04)and IBS-D and IBS-M subjects (-4.08±0.90 vs-3.08±1.38,P=0.05).Furthermore,a phylotype with 94%similarity to R.torques was more prevalent in IBS-D patients'intestinal micro- biota than in that of control subjects(-2.43±1.49 vs -4.02±1.63,P=0.01).A phylotype with 93%simi- larity to R.torques was associated with control sam- ples when compared with IBS-M(-2.41±0.53 vs -2.92±0.56,P=0.00).Additionally,a R.bromii-like phylotype was associated with IBS-C patients in com- parison to control subjects(-1.61±1.83 vs-3.69± 2.42,P=0.01).All of the above mentioned phylotype specific alterations were independent of the effect of time. CONCLUSION:Significant phylotype level alterationsin the intestinal microbiotas of IBS patients were observed,further emphasizing the possible contribution of the gastrointestinal microbiota in IBS.展开更多
Vast viruses are thought to be associated with mosquitoes.Anopheles sinensis,Armigeres subalbatus,Culex quinquefasciatus,and Culex tritaeniorhynchus are very common mosquito species in China,and whether the virome str...Vast viruses are thought to be associated with mosquitoes.Anopheles sinensis,Armigeres subalbatus,Culex quinquefasciatus,and Culex tritaeniorhynchus are very common mosquito species in China,and whether the virome structure in each species is species-specific has not been evaluated.In this study,a total of 2222 mosquitoes were collected from the same geographic location,and RNAs were sequenced using the Illumina Miseq platform.After querying to the Refseq database,a total of 3,435,781,2,223,509,5,727,523,and 6,387,867 paired-end reads were classified under viral sequences from An.sinensis,Ar.subalbatus,Cx.quinquefasciatus,and Cx.tritaeniorhynchus,respectively,with the highest prevalence of virus-associated reads being observed in Cx.quinquefasciatus.The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families,together with an unclassified group of viruses.Anelloviridae,Circoviridae,Genomoviridae,Iridoviridae,Mesoniviridae,Microviridae,Myoviridae,Parvoviridae,Phenuiviridae,and Podoviridae were the top ten significantly different viral families among the four species.Further analysis reveals that the virome is species-specific in four mosquito samples,and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes.This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.展开更多
基金Supported by The Finnish Funding Agency for Technologyand Innovation,Tekes,grants No.945/401/00 and 40160/05the Finnish Graduate School of Applied Biosciences,the Academy of Finland,Grant No.214 157the Centre of Excellence on Microbial Food Safety Research,Academy of Finland
文摘AIM:To study whether selected bacterial 16S ribosomal RNA(rRNA)gene phylotypes are capable of disting- uishing irritable bowel syndrome(IBS). METHODS:The faecal microbiota of twenty volunteers with IBS,subdivided into eight diarrhoea-predominant (IBS-D),eight constipation-predominant(IBS-C)and four mixed symptom-subtype(IBS-M)IBS patients,and fifteen control subjects,were analysed at three time-points with a set of fourteen quantitative real-timepolymerase chain reaction assays.All assays targeted 16S rRNA gene phylotypes putatively associated with IBS,based on 16S rRNA gene library sequence analysis. The target phylotypes were affiliated with Actinobac-teria,Bacteroidetes and Firmicutes.Eight of the target phylotypes had less than 95%similarity to cultured bacterial species according to their 16S rRNA gene sequence.The data analyses were made with repeated-measures ANCOVA-type modelling of the data and principle component analysis(PCA)with linear mixed-effects models applied to the principal component scores. RESULTS:Bacterial phylotypes Clostridium cocleatum 88%,Clostridium thermosuccinogenes 85%,Coprobacillus catenaformis 91%,Ruminococcus bromii-like, Ruminococcus torques 91%,and R.torques 93%were detected from all samples analysed.A multivariate analysis of the relative quantities of all 14 bacterial 16S rRNA gene phylotypes suggested that the intestinal microbiota of the IBS-D patients differed from other sample groups.The PCA on the first principal component(PC1),explaining 30.36%of the observed variation in the IBS-D patient group,was significantly altered from all other sample groups(IBS-D vs control, P=0.01;IBS-D vs IBS-M,P=0.00;IBS-D vs IBS-C, P=0.05).Significant differences were also observed in the levels of distinct phylotypes using relative values in proportion to the total amount of bacteria.A phy- lotype with 85%similarity to C.thermosuccinogenes was quantified in significantly different quantities among the IBS-D and control subjects(-4.08±0.90 vs -3.33±1.16,P=0.04)and IBS-D and IBS-M subjects (-4.08±0.90 vs-3.08±1.38,P=0.05).Furthermore,a phylotype with 94%similarity to R.torques was more prevalent in IBS-D patients'intestinal micro- biota than in that of control subjects(-2.43±1.49 vs -4.02±1.63,P=0.01).A phylotype with 93%simi- larity to R.torques was associated with control sam- ples when compared with IBS-M(-2.41±0.53 vs -2.92±0.56,P=0.00).Additionally,a R.bromii-like phylotype was associated with IBS-C patients in com- parison to control subjects(-1.61±1.83 vs-3.69± 2.42,P=0.01).All of the above mentioned phylotype specific alterations were independent of the effect of time. CONCLUSION:Significant phylotype level alterationsin the intestinal microbiotas of IBS patients were observed,further emphasizing the possible contribution of the gastrointestinal microbiota in IBS.
基金supported by the Ministry of Science and Technology of China (Science and Technology Basic Work Program 2013FY113500)
文摘Vast viruses are thought to be associated with mosquitoes.Anopheles sinensis,Armigeres subalbatus,Culex quinquefasciatus,and Culex tritaeniorhynchus are very common mosquito species in China,and whether the virome structure in each species is species-specific has not been evaluated.In this study,a total of 2222 mosquitoes were collected from the same geographic location,and RNAs were sequenced using the Illumina Miseq platform.After querying to the Refseq database,a total of 3,435,781,2,223,509,5,727,523,and 6,387,867 paired-end reads were classified under viral sequences from An.sinensis,Ar.subalbatus,Cx.quinquefasciatus,and Cx.tritaeniorhynchus,respectively,with the highest prevalence of virus-associated reads being observed in Cx.quinquefasciatus.The metagenomic comparison analysis showed that the virus-related reads were distributed across 26 virus families,together with an unclassified group of viruses.Anelloviridae,Circoviridae,Genomoviridae,Iridoviridae,Mesoniviridae,Microviridae,Myoviridae,Parvoviridae,Phenuiviridae,and Podoviridae were the top ten significantly different viral families among the four species.Further analysis reveals that the virome is species-specific in four mosquito samples,and several viral sequences which maybe belong to novel viruses are discovered for the first time in those mosquitoes.This investigation provides a basis for a comprehensive knowledge on the mosquito virome status in China.
