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 mai...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.展开更多
Objective Antimicrobial resistance(AMR)has become a global concern and is especially severe in China.To effectively and reliably provide AMR data,we developed a new high-throughput real-time PCR assay based on microfl...Objective Antimicrobial resistance(AMR)has become a global concern and is especially severe in China.To effectively and reliably provide AMR data,we developed a new high-throughput real-time PCR assay based on microfluidic dynamic technology,and screened multiple AMR genes in broiler fecal samples.Methods A high-throughput real-time PCR system with an new designed integrated fluidic circuit assay were performed AMR gene detection.A total of 273 broiler fecal samples collected from two geographically separated farms were screened AMR genes.Results The new assay with limits of detection ranging from 40.9 to 8,000 copies/reaction.The sensitivity rate,specificity rate,positive predictive value,negative predictive value and correct indices were 99.30%,98.08%,95.31%,99.79%,and 0.9755,respectively.Utilizing this assay,we demonstrate that AMR genes are widely spread,with positive detection rates ranging from 0 to 97.07%in 273 broiler fecal samples.bla CTX-M,bla TEM,mcr-1,fex A,cfr,optr A,and int I1 showed over 80%prevalence.The dissemination of AMR genes was distinct between the two farms.Conclusions We successfully established a new high-throughput real-time PCR assay applicable to AMR gene surveillance from fecal samples.The widespread existence of AMR genes detected in broiler farms highlights the current and severe problem of AMR.展开更多
Dear Editor,Porcine astrovirus(PAstV)is a swine enteric virus which can cause diarrhea and vomiting in pigs,particularly in neonatal piglets(Fang et al.,2019;Su etal.,2020).PAstVwasfirstdetectedby electron microscopyi...Dear Editor,Porcine astrovirus(PAstV)is a swine enteric virus which can cause diarrhea and vomiting in pigs,particularly in neonatal piglets(Fang et al.,2019;Su etal.,2020).PAstVwasfirstdetectedby electron microscopyinthe fecal samples from diarrheal piglets in 1980(Bridger,1980).Based on viral genomes,PAstV is divided into five distinct genotypes(PAstV1-PAstV5)(Fang et al.,2019;Mi et al.,2020;Su et al.,2020).The PAstV5 was the main genotype prevalent in China.Xiao reported a positivity rate of 24.8%for PAstV5 as the predominant genotype in Hunan Province(Xiao et al.,2017).Cai reported a positive rate of 7.5%for PAstV5 in Sichuan Province(Cai et al.,2016).A study in Yunnan Province revealed a total infection rate of 39.9%for PAstV2 and PAstV5(Ren et al.,2022).The PAstV genome open read frame 2(ORF2)encodes for a~90 kDa structural polyprotein called capsid protein(Cap)(Arias and DuBois,2017).The region including amino acids(aa)1-415(N-terminus)of the Cap ishighly conserved,and the region starting at aa 416(C-terminus)is extremely variable(Ren et al.,2022).Moreover,the Cap can bind to host cell receptors and is the main target of neutralizing antibodies(Ricemeyer et al.,2022).展开更多
Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with a cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivor...Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with a cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivorous livestock animals. Also, other Taeniid tapeworms could infect domestic dogs and they pose significant veterinary and public health concerns worldwide. This study aimed to develop a sensitive molecular method for detecting Echinococcus spp. DNA in dog fecal samples using next-generation sequencing (NGS). A set of PCR primers targeting conserved regions of Taeniid tapeworms’ 18s rRNA genes was designed and tested for amplifying genomic DNA from various tapeworm species. The PCR system demonstrated high sensitivity, amplifying DNA from all tested tapeworm species, with differences observed in amplified band sizes. The primers were adapted for NGS analysis by adding forward and reverse adapters, enabling the sequencing of amplified DNA fragments. Application of the developed PCR system to dog fecal samples collected from Yatta town, Palestine, revealed the presence of E. granulosus DNA in five out of 50 samples. NGS analysis confirmed the specificity of the amplified DNA fragments, showing 98% - 99% similarity with the 18s rDNA gene of E. granulosus. This study demonstrates the utility of NGS-based molecular methods for accurate and sensitive detection of Echinococcus spp. in dog fecal samples, providing valuable insights for epidemiological surveillance and control programs of echinococcosis in endemic regions.展开更多
BACKGROUND Colorectal cancer(CRC),the third most common cause of death in both males and females worldwide,shows a positive response to therapy and usually a better prognosis when detected at an early stage.However,th...BACKGROUND Colorectal cancer(CRC),the third most common cause of death in both males and females worldwide,shows a positive response to therapy and usually a better prognosis when detected at an early stage.However,the survival rate declines when the diagnosis is late and the tumor spreads to other organs.Currently,the measures widely used in the clinic are fecal occult blood test and evaluation of serum tumor markers,but the lack of sensitivity and specificity of these markers restricts their use for CRC diagnosis.Due to its high sensitivity and precision,colonoscopy is currently the gold-standard screening technique for CRC,but it is a costly and invasive procedure.Therefore,the implementation of custom-made methodologies including those with minimal invasiveness,protection,and reproducibility is highly desirable.With regard to other screening methods,the screening of fecal samples has several benefits,and metabolomics is a successful method to classify the metabolite shift in living systems as a reaction to pathophysiological influences,genetic modifications,and environmental factors.AIM To characterize the variation groups and potentially recognize some diagnostic markers,we compared with healthy controls(HCs)the fecal nuclear magnetic resonance(NMR)metabolomic profiles of patients with CRC or adenomatous polyposis(AP).METHODS Proton nuclear magnetic resonance spectroscopy was used in combination with multivariate and univariate statistical approaches,to define the fecal metabolic profiles of 32 CRC patients,16 AP patients,and 38 HCs well matched in age,sex,and body mass index.RESULTS NMR metabolomic analyses revealed that fecal sample profiles differed among CRC patients,AP patients,and HCs,and some discriminatory metabolites including acetate,butyrate,propionate,3-hydroxyphenylacetic acid,valine,tyrosine and leucine were identified.CONCLUSION In conclusion,we are confident that our data can be a forerunner for future studies on CRC management,especially the diagnosis and evaluation of the effectiveness of treatments.展开更多
Background： The effect of time of fecal sampling on the accuracy of acid-detergent insoluble ash （ADIA） and alkaline-peroxide lignin （APL） for the prediction of fecal output （FO） in cattle was evaluated. Eight ...Background： The effect of time of fecal sampling on the accuracy of acid-detergent insoluble ash （ADIA） and alkaline-peroxide lignin （APL） for the prediction of fecal output （FO） in cattle was evaluated. Eight ruminally cannulated cows （594 _＋ 35.5 kg） were allocated randomly to 4 bermudagrass [Cynodon dactylon （L.） Pers.] hay diets markedly different in crude protein concentration （79-164 g/kg） with 2 replicates per diet for 3 periods. Cows were offered hay individually at 20 g DM/kg of body weight daily in equal feedings at 08：00 and 16：00 h for a 10-d adaptation period followed by 5-d of total fecal collection. Fecal grab samples also were taken each day during the fecal collection period at 06：00, 12：00, 18：00, and 24：00 h either directly from the rectum or from freshly voided feces. Samples were composited within cow and time across the 5 d total fecal collection period. Additionally, forage, ort, and fecal samples were analyzed for concentrations of APL and ADIA. Results： Fecal concentrations of ADIA and APL were not affected by sampling time （P 〉 0.22）, even though diet affected （P 〈 0.01） fecal ADIA and APL concentrations. There were no diet x sampling time interactions （P ≥ 0.60）. Estimates of FO and dry matter digestibility （DMD） from ADIA and APL were not affected （P 〉 0.16） by sampling time or the diet x sampling time interaction （P 〉 0.74）. Estimates of FO and DMD from markers from different sampling times or all different combinations of sampling time were not different （P 〉 0.72） from those of total collection among internal markers. Conclusion： Little variation in concentrations of ADIA and APL in daily fecal excretion across time increases flexibility in fecal grab sampling schedules for predicting FO and DMD.展开更多
Birds maintain complex and intimate associations with a diverse community of microbes in their intestine.Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multi...Birds maintain complex and intimate associations with a diverse community of microbes in their intestine.Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses.However,the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings.Through performing a network meta-analysis for 13 published bird gut microbiome studies,here we attempt to investigate the comparability of these invasive and non-invasive sampling methods.The two most used non-invasive sampling methods(cloacal swabs and fecal samples)showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples.Overall,non-invasive samples showed decreased alpha diversity compared to intestinal samples,but the alpha diversities of fecal samples were more comparable to the intestinal samples.On the contrary,the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples,but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples.Phylogenetic status,diet,and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples.Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa,while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions.The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes.展开更多
Objective To explore the effect of CLP-1 receptor agonist(CLP-1 RA)on the intestinal flora of overweight or obese patients with type 2 diabetes mellitus(T2DM).Methods 20 newly diagnosed overweight/obese T2DM patients ...Objective To explore the effect of CLP-1 receptor agonist(CLP-1 RA)on the intestinal flora of overweight or obese patients with type 2 diabetes mellitus(T2DM).Methods 20 newly diagnosed overweight/obese T2DM patients hospitalized in our hospital from September 2022 to February 2023,were treated with GLP-1RA Liraglutide for 3 months.General data and clinical indicators were collected before and after treatment respectively.16SrDNA high-throughputtsequencing was used to detect intestinal flora in fecal samples.RIesults Compared with group A,body weight,BMI,TC,TG,LDL-C,SBP,FPG,HbA,c and insulin resistance index(HOMA-IR)were decreased in group B(P<0.05),islet beta cell function index(HOMA-β)and HDL-C were increased(P<0.05).There was no change in the a diversity of intestinal flora(P>0.05).Theβdiversity showed a clustered distribution.After treatment,the abundance of Betaproteobacteria,Pasteurellales,Pasteurellaceae,Clostridiaceae,Romboutsia,Clostridium,Peptostreptococcaceae,Haemophilus,Solobacterium,Bacteroides-cellulosilyticus increased.The abundance of Burkholderiales,Enterococcaceae andEnterococcus decreased.At the genus level,the abundance of Clostridium,Haemophilus,Romboutsia and Megamonas increased(P<O.05).Conclusion GLP-1RA can not only improve glucose and lipid metabolism,βcell function and insulin sensitivity in overweight/obese T2DM patients,but can also increase the abundance of beneficial bacteriaa and reduce the abundance of pathogenic bacteria.展开更多
The role of the gut microbiome in enhancing the efficacy of anticancer treatments like chemotherapy and radiotherapy is well acknowledged.However,there is limited empirical evidence on its predictive capabilities for ...The role of the gut microbiome in enhancing the efficacy of anticancer treatments like chemotherapy and radiotherapy is well acknowledged.However,there is limited empirical evidence on its predictive capabilities for neoadjuvant immunochemotherapy(NICT)responses in esophageal squamous cell carcinoma(ESCC).Our study fills this gap by comprehensively analyzing the gut microbiome's influence on NICT outcomes.We analyzed 16S rRNA gene sequences from 136 fecal samples from 68 ESCC patients before and after NICT,along with 19 samples from healthy controls.After NICT,marked microbiome composition changes were noted,including a decrease in EScC-associated pathogens and an increase in beneficial microbes such as Limosilactobacillus,Lacticaseibacillus,and Staphylococcus.Baseline microbiota profiles effectively differentiated responders from nonresponders,with responders showing higher levels of short-chain fatty acid(SCFA)-producing bacteria such as Faecalibacterium,Eubacterium_eligens_group,Anaerostipes,and Odoribacter,and nonresponders showing increases in Veillonella,Campylobacter,Atopobium,and Trichococcus.We then divided our patient cohort into training and test sets at a 4:1 ratio and utilized the XGBoost-RFE algorithm to identify 7 key microbial biomarkers-Faecalibacterium,Subdoligranulum,Veillonella,Hungatella,Odoribacter,Butyricicoccus,and HTO02.Apredictive model was developed using LightGBM,which achieved an area under the receiver operating characteristic curve(AUC)of 86.8%[95%confidence interval(CI).73.8%to 99.4%] in the training set,76.8%(95%Cl,41.2%to 99.7%)in the validation set,and 76.5%(95%Cl,50.4%to 100%)in the testing set.Our findings underscore the gut microbiome as a novel source of biomarkers for predicting NICT responses in ESCc,highlighting its potential to enhance personalized treatment strategies and advance the integration of microbiome profiling into clinical practice for modulating cancer treatment responses.展开更多
Fecal samples or cloacal swabs are preferred over lethal dissections to study vertebrate gut microbiota for ethical reasons,but it remains unclear which nonlethal methods provide more accurate information about gut mi...Fecal samples or cloacal swabs are preferred over lethal dissections to study vertebrate gut microbiota for ethical reasons,but it remains unclear which nonlethal methods provide more accurate information about gut microbiota.We compared the bacterial communities of three gastrointestinal tract(GIT)segments,that is,stomach,small intestine(midgut),and rectum(hindgut)with the bacterial communities of the cloaca and feces in the mesquite lizard Sceloporus grammicus.The hindgut had the highest taxonomic and functional alpha diversity,followed by midgut and feces,whereas the stomach and cloaca showed the lowest diversities.The taxonomic assemblages of the GIT segments at the phylum level were strongly correlated with those retrieved from feces and cloacal swabs(rs>0.84 in all cases).The turnover ratio of Amplicon Sequence Variants(ASVs)between midgut and hindgut and the feces was lower than the ratio between these segments and the cloaca.More than half of the core-ASVs in the midgut(24 of 32)and hindgut(58 of 97)were also found in feces,while less than 5 were found in the cloaca.At the ASVs level,however,the structure of the bacterial communities of the midgut and hindgut were similar to those detected in feces and cloaca.Our findings suggest that fecal samples and cloacal swabs of spiny lizards provide a good approximation of the taxonomic assemblages and beta diversity of midgut and hindgut microbiota,while feces better represent the bacterial communities of the intestinal segments at a single nucleotide variation level than cloacal swabs.展开更多
基金supported by Jiangsu Provincial Key Research and Development Projects No.BE2017693National Natural Science Foundation of China No.81741062
文摘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.
基金supported by the National Natural Science Foundation of China [Grant agreement 31502124]the National Science and Technology Major Project of China [Grant agreement 2018ZX10733402]
文摘Objective Antimicrobial resistance(AMR)has become a global concern and is especially severe in China.To effectively and reliably provide AMR data,we developed a new high-throughput real-time PCR assay based on microfluidic dynamic technology,and screened multiple AMR genes in broiler fecal samples.Methods A high-throughput real-time PCR system with an new designed integrated fluidic circuit assay were performed AMR gene detection.A total of 273 broiler fecal samples collected from two geographically separated farms were screened AMR genes.Results The new assay with limits of detection ranging from 40.9 to 8,000 copies/reaction.The sensitivity rate,specificity rate,positive predictive value,negative predictive value and correct indices were 99.30%,98.08%,95.31%,99.79%,and 0.9755,respectively.Utilizing this assay,we demonstrate that AMR genes are widely spread,with positive detection rates ranging from 0 to 97.07%in 273 broiler fecal samples.bla CTX-M,bla TEM,mcr-1,fex A,cfr,optr A,and int I1 showed over 80%prevalence.The dissemination of AMR genes was distinct between the two farms.Conclusions We successfully established a new high-throughput real-time PCR assay applicable to AMR gene surveillance from fecal samples.The widespread existence of AMR genes detected in broiler farms highlights the current and severe problem of AMR.
基金supported by grants from the Henan Province Key Research and Development Special Project(231111113100)the Henan Province Natural Science Foundation Interdisciplinary Innovation Research Group Project(232300421001)the Postgraduate Education Reform and Quality Improvement Project of Henan Province(YJS2023SZ13).
文摘Dear Editor,Porcine astrovirus(PAstV)is a swine enteric virus which can cause diarrhea and vomiting in pigs,particularly in neonatal piglets(Fang et al.,2019;Su etal.,2020).PAstVwasfirstdetectedby electron microscopyinthe fecal samples from diarrheal piglets in 1980(Bridger,1980).Based on viral genomes,PAstV is divided into five distinct genotypes(PAstV1-PAstV5)(Fang et al.,2019;Mi et al.,2020;Su et al.,2020).The PAstV5 was the main genotype prevalent in China.Xiao reported a positivity rate of 24.8%for PAstV5 as the predominant genotype in Hunan Province(Xiao et al.,2017).Cai reported a positive rate of 7.5%for PAstV5 in Sichuan Province(Cai et al.,2016).A study in Yunnan Province revealed a total infection rate of 39.9%for PAstV2 and PAstV5(Ren et al.,2022).The PAstV genome open read frame 2(ORF2)encodes for a~90 kDa structural polyprotein called capsid protein(Cap)(Arias and DuBois,2017).The region including amino acids(aa)1-415(N-terminus)of the Cap ishighly conserved,and the region starting at aa 416(C-terminus)is extremely variable(Ren et al.,2022).Moreover,the Cap can bind to host cell receptors and is the main target of neutralizing antibodies(Ricemeyer et al.,2022).
文摘Cystic echinococcosis (CE) is a prevalent zoonotic disease caused by Echinococcus granulosus, with a cosmopolitan distribution. The parasite is transmitted cyclically between canines and numerous intermediate herbivorous livestock animals. Also, other Taeniid tapeworms could infect domestic dogs and they pose significant veterinary and public health concerns worldwide. This study aimed to develop a sensitive molecular method for detecting Echinococcus spp. DNA in dog fecal samples using next-generation sequencing (NGS). A set of PCR primers targeting conserved regions of Taeniid tapeworms’ 18s rRNA genes was designed and tested for amplifying genomic DNA from various tapeworm species. The PCR system demonstrated high sensitivity, amplifying DNA from all tested tapeworm species, with differences observed in amplified band sizes. The primers were adapted for NGS analysis by adding forward and reverse adapters, enabling the sequencing of amplified DNA fragments. Application of the developed PCR system to dog fecal samples collected from Yatta town, Palestine, revealed the presence of E. granulosus DNA in five out of 50 samples. NGS analysis confirmed the specificity of the amplified DNA fragments, showing 98% - 99% similarity with the 18s rDNA gene of E. granulosus. This study demonstrates the utility of NGS-based molecular methods for accurate and sensitive detection of Echinococcus spp. in dog fecal samples, providing valuable insights for epidemiological surveillance and control programs of echinococcosis in endemic regions.
文摘BACKGROUND Colorectal cancer(CRC),the third most common cause of death in both males and females worldwide,shows a positive response to therapy and usually a better prognosis when detected at an early stage.However,the survival rate declines when the diagnosis is late and the tumor spreads to other organs.Currently,the measures widely used in the clinic are fecal occult blood test and evaluation of serum tumor markers,but the lack of sensitivity and specificity of these markers restricts their use for CRC diagnosis.Due to its high sensitivity and precision,colonoscopy is currently the gold-standard screening technique for CRC,but it is a costly and invasive procedure.Therefore,the implementation of custom-made methodologies including those with minimal invasiveness,protection,and reproducibility is highly desirable.With regard to other screening methods,the screening of fecal samples has several benefits,and metabolomics is a successful method to classify the metabolite shift in living systems as a reaction to pathophysiological influences,genetic modifications,and environmental factors.AIM To characterize the variation groups and potentially recognize some diagnostic markers,we compared with healthy controls(HCs)the fecal nuclear magnetic resonance(NMR)metabolomic profiles of patients with CRC or adenomatous polyposis(AP).METHODS Proton nuclear magnetic resonance spectroscopy was used in combination with multivariate and univariate statistical approaches,to define the fecal metabolic profiles of 32 CRC patients,16 AP patients,and 38 HCs well matched in age,sex,and body mass index.RESULTS NMR metabolomic analyses revealed that fecal sample profiles differed among CRC patients,AP patients,and HCs,and some discriminatory metabolites including acetate,butyrate,propionate,3-hydroxyphenylacetic acid,valine,tyrosine and leucine were identified.CONCLUSION In conclusion,we are confident that our data can be a forerunner for future studies on CRC management,especially the diagnosis and evaluation of the effectiveness of treatments.
基金supported by University of Arkansas Division of Agriculturethe Robert S.McNamara Fellowship program of the World Bank
文摘Background： The effect of time of fecal sampling on the accuracy of acid-detergent insoluble ash （ADIA） and alkaline-peroxide lignin （APL） for the prediction of fecal output （FO） in cattle was evaluated. Eight ruminally cannulated cows （594 _＋ 35.5 kg） were allocated randomly to 4 bermudagrass [Cynodon dactylon （L.） Pers.] hay diets markedly different in crude protein concentration （79-164 g/kg） with 2 replicates per diet for 3 periods. Cows were offered hay individually at 20 g DM/kg of body weight daily in equal feedings at 08：00 and 16：00 h for a 10-d adaptation period followed by 5-d of total fecal collection. Fecal grab samples also were taken each day during the fecal collection period at 06：00, 12：00, 18：00, and 24：00 h either directly from the rectum or from freshly voided feces. Samples were composited within cow and time across the 5 d total fecal collection period. Additionally, forage, ort, and fecal samples were analyzed for concentrations of APL and ADIA. Results： Fecal concentrations of ADIA and APL were not affected by sampling time （P 〉 0.22）, even though diet affected （P 〈 0.01） fecal ADIA and APL concentrations. There were no diet x sampling time interactions （P ≥ 0.60）. Estimates of FO and dry matter digestibility （DMD） from ADIA and APL were not affected （P 〉 0.16） by sampling time or the diet x sampling time interaction （P 〉 0.74）. Estimates of FO and DMD from markers from different sampling times or all different combinations of sampling time were not different （P 〉 0.72） from those of total collection among internal markers. Conclusion： Little variation in concentrations of ADIA and APL in daily fecal excretion across time increases flexibility in fecal grab sampling schedules for predicting FO and DMD.
基金funded by the National Natural Science Foundation of China(31870370)the Key Grant of Guangxi Nature and Science Foundation(2018GXNSFDA281016)。
文摘Birds maintain complex and intimate associations with a diverse community of microbes in their intestine.Multiple invasive and non-invasive sampling methods are used to characterize these communities to answer a multitude of eco-evolutionary questions related to host-gut microbiome symbioses.However,the comparability of these invasive and non-invasive sampling methods is sparse with contradicting findings.Through performing a network meta-analysis for 13 published bird gut microbiome studies,here we attempt to investigate the comparability of these invasive and non-invasive sampling methods.The two most used non-invasive sampling methods(cloacal swabs and fecal samples)showed significantly different results in alpha diversity and taxonomic relative abundances compared to invasive samples.Overall,non-invasive samples showed decreased alpha diversity compared to intestinal samples,but the alpha diversities of fecal samples were more comparable to the intestinal samples.On the contrary,the cloacal swabs characterized significantly lower alpha diversities than in intestinal samples,but the taxonomic relative abundances acquired from cloacal swabs were similar to the intestinal samples.Phylogenetic status,diet,and domestication degree of host birds also influenced the differences in microbiota characterization between invasive and non-invasive samples.Our results indicate a general pattern in microbiota differences among intestinal mucosal and non-invasive samples across multiple bird taxa,while highlighting the importance of evaluating the appropriateness of the microbiome sampling methods used to answer specific research questions.The overall results also suggest the potential importance of using both fecal and cloacal swab sampling together to properly characterize bird microbiomes.
文摘Objective To explore the effect of CLP-1 receptor agonist(CLP-1 RA)on the intestinal flora of overweight or obese patients with type 2 diabetes mellitus(T2DM).Methods 20 newly diagnosed overweight/obese T2DM patients hospitalized in our hospital from September 2022 to February 2023,were treated with GLP-1RA Liraglutide for 3 months.General data and clinical indicators were collected before and after treatment respectively.16SrDNA high-throughputtsequencing was used to detect intestinal flora in fecal samples.RIesults Compared with group A,body weight,BMI,TC,TG,LDL-C,SBP,FPG,HbA,c and insulin resistance index(HOMA-IR)were decreased in group B(P<0.05),islet beta cell function index(HOMA-β)and HDL-C were increased(P<0.05).There was no change in the a diversity of intestinal flora(P>0.05).Theβdiversity showed a clustered distribution.After treatment,the abundance of Betaproteobacteria,Pasteurellales,Pasteurellaceae,Clostridiaceae,Romboutsia,Clostridium,Peptostreptococcaceae,Haemophilus,Solobacterium,Bacteroides-cellulosilyticus increased.The abundance of Burkholderiales,Enterococcaceae andEnterococcus decreased.At the genus level,the abundance of Clostridium,Haemophilus,Romboutsia and Megamonas increased(P<O.05).Conclusion GLP-1RA can not only improve glucose and lipid metabolism,βcell function and insulin sensitivity in overweight/obese T2DM patients,but can also increase the abundance of beneficial bacteriaa and reduce the abundance of pathogenic bacteria.
基金supported by the National Nature Science Foundation of China(nos.82303178 and 82200612)the Shenzhen Science and Technology Program(grant nos.JCYJ20220530154012028 and RCBS20221008093243060)the Guangdong Basic and Applied Basic Research Foundation(no.2021A1515110216).
文摘The role of the gut microbiome in enhancing the efficacy of anticancer treatments like chemotherapy and radiotherapy is well acknowledged.However,there is limited empirical evidence on its predictive capabilities for neoadjuvant immunochemotherapy(NICT)responses in esophageal squamous cell carcinoma(ESCC).Our study fills this gap by comprehensively analyzing the gut microbiome's influence on NICT outcomes.We analyzed 16S rRNA gene sequences from 136 fecal samples from 68 ESCC patients before and after NICT,along with 19 samples from healthy controls.After NICT,marked microbiome composition changes were noted,including a decrease in EScC-associated pathogens and an increase in beneficial microbes such as Limosilactobacillus,Lacticaseibacillus,and Staphylococcus.Baseline microbiota profiles effectively differentiated responders from nonresponders,with responders showing higher levels of short-chain fatty acid(SCFA)-producing bacteria such as Faecalibacterium,Eubacterium_eligens_group,Anaerostipes,and Odoribacter,and nonresponders showing increases in Veillonella,Campylobacter,Atopobium,and Trichococcus.We then divided our patient cohort into training and test sets at a 4:1 ratio and utilized the XGBoost-RFE algorithm to identify 7 key microbial biomarkers-Faecalibacterium,Subdoligranulum,Veillonella,Hungatella,Odoribacter,Butyricicoccus,and HTO02.Apredictive model was developed using LightGBM,which achieved an area under the receiver operating characteristic curve(AUC)of 86.8%[95%confidence interval(CI).73.8%to 99.4%] in the training set,76.8%(95%Cl,41.2%to 99.7%)in the validation set,and 76.5%(95%Cl,50.4%to 100%)in the testing set.Our findings underscore the gut microbiome as a novel source of biomarkers for predicting NICT responses in ESCc,highlighting its potential to enhance personalized treatment strategies and advance the integration of microbiome profiling into clinical practice for modulating cancer treatment responses.
基金The authors thank Dr.Luc Dendooven for his valuable comments on the manuscript,and Estación Científica La Malinche and Centro Tlaxcala de Biología de la Conducta for access and logistic support.This research was funded by Consejo Nacional de Ciencia y Tecnología(CONACyT),Ciencia de Frontera(project number:137748)Infraestructura(project number:205945)the Cátedras CONACyT program(project number:883).M.H.received a Ph.D.scholarship number:967648 and S.H-.P.a postdoctoral grant number:929602 by CONACyT.This article is a requirement for obtaining a Ph.D.degree of the first author.
文摘Fecal samples or cloacal swabs are preferred over lethal dissections to study vertebrate gut microbiota for ethical reasons,but it remains unclear which nonlethal methods provide more accurate information about gut microbiota.We compared the bacterial communities of three gastrointestinal tract(GIT)segments,that is,stomach,small intestine(midgut),and rectum(hindgut)with the bacterial communities of the cloaca and feces in the mesquite lizard Sceloporus grammicus.The hindgut had the highest taxonomic and functional alpha diversity,followed by midgut and feces,whereas the stomach and cloaca showed the lowest diversities.The taxonomic assemblages of the GIT segments at the phylum level were strongly correlated with those retrieved from feces and cloacal swabs(rs>0.84 in all cases).The turnover ratio of Amplicon Sequence Variants(ASVs)between midgut and hindgut and the feces was lower than the ratio between these segments and the cloaca.More than half of the core-ASVs in the midgut(24 of 32)and hindgut(58 of 97)were also found in feces,while less than 5 were found in the cloaca.At the ASVs level,however,the structure of the bacterial communities of the midgut and hindgut were similar to those detected in feces and cloaca.Our findings suggest that fecal samples and cloacal swabs of spiny lizards provide a good approximation of the taxonomic assemblages and beta diversity of midgut and hindgut microbiota,while feces better represent the bacterial communities of the intestinal segments at a single nucleotide variation level than cloacal swabs.
