BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of ...BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.展开更多
Objective: To explore the change of intestinal microecology in patients with primary Sjogren’s syndrome(p SS) and correlation with disease activity, and also discuss the therapy effect of Yangyin Yiqi Huoxue Recipe(...Objective: To explore the change of intestinal microecology in patients with primary Sjogren’s syndrome(p SS) and correlation with disease activity, and also discuss the therapy effect of Yangyin Yiqi Huoxue Recipe(养阴益气活血方, YYHD). Methods: Sixteen p SS patients were enrolled in the present study, who received 3-month treatment of YYHR, 200 mL orally twice daily. Their pre-and post-test ESSDAI scores, erythrocyte sedimentation rate(ESR) and serum immunoglobulin G(IgG) levels were measured respectively. The 16 Sr DNA metagenomic sequencing was used to detect and analyze the abundance and diversity of intestinal bacteria flora and the proportion of bacteria at the levels of phylum, family, and genus, in comparision with those of 6 healthy subjects in the control group. Results: The abundance and diversity of intestinal bacteria flora in pSS patients were lower than those of healthy subjects(P<0.05). After the treatment with YYHD, patients’ ESSDAI score and levels of IgG and ESR have decreased significantly(P<0.05). At the phylum level, the proportions of Actinobacteria, Firmicutes, Fusobacteria and Proteobacteria have reduced sharply, while the proportions of Bacteroidetes, Teneriquetes and Candidate-division-TM7 have increased significantly by treatment(all P<0.05). At the classification level, such treatment has caused a significant decrease in the proportions of Bacteroidaceae, Ruminococcaceae, Veillonellaceae, and Enterobacteriacea(all P<0.05), but a significant increase in the proportion of Lachnospiraceae(P<0.05). At the genus level, the treatment has significantly decreased the proportions of Bifidobacterium, Bacteroides, Escherichia-Shigella, Faecalibacterium and Prevotella(all P<0.05), but significantly increased the proportion of Clostridia(P<0.05), close to the levels of healthy subjects(P>0.05). Conclusions: There exists an imbalance of intestinal microecology in p SS patients, which can be improved through the treatment with YYHD. Besides, such treatment can also improve the disease ac展开更多
BACKGROUND Chlamydia psittaci(C.psittaci)is a gram-negative intracellular parasitic pathogenic bacterium that can infect avian and mammalian hosts,including humans.The detection of C.psittaci infections typically reli...BACKGROUND Chlamydia psittaci(C.psittaci)is a gram-negative intracellular parasitic pathogenic bacterium that can infect avian and mammalian hosts,including humans.The detection of C.psittaci infections typically relies on traditional antigen-based immunoassays or serological testing that often lack sensitivity and/or specificity.Metagenomic next generation sequencing(mNGS)is an emerging tool for diagnosis.AIM To demonstrate that mNGS represents a valuable tool for rapid,sensitive,and accurate pathogen detection including C.psittaci infections.METHODS Four cases of psittacosis pneumonia and one case of pediatric psittacosis meningitis were diagnosed between December 2019 and May 2020 using mNGS at Changzhou Second People’s Hospital affiliated to Nanjing Medical University.Patients’clinical characteristics,manifestations,and treatment histories were retrospectively evaluated.RESULTS All five patients had a history of exposure to wild(psittacine or other birds)or domesticated birds(chickens).All patients had a high fever(>39℃)and three of them(60%)experienced organ insufficiency during the disease.The laboratory data showed normal to slightly increased leucocyte and neutrophil counts,and elevated procalcitonin levels in all five cases,and very high C-reactive protein levels in psittacosis pneumonia patients.mNGS identified a potential pathogen,C.psittaci,in patients’bronchoalveolar lavage fluid or cerebrospinal fluid.Computed tomography revealed lung air-space consolidation,pleural thickening,and effusion fluid buildup in psittacosis pneumonia cases,and an arachnoid cyst in the right temporal lobe of the pediatric psittacosis meningitis patient.All patients experienced complete recovery following the administration of targeted antichlamydia therapy.CONCLUSION This study not only demonstrated that mNGS represents a valuable tool for rapid,sensitive,and accurate pathogen detection,but also raised public health concerns over C.psittaci infections.展开更多
Increasing evidence suggests that food ingested polyphenols can have beneficial effects in neuronal protection acting against oxidative stress and inflammatory injury. Moreover, polyphenols have been reported to promo...Increasing evidence suggests that food ingested polyphenols can have beneficial effects in neuronal protection acting against oxidative stress and inflammatory injury. Moreover, polyphenols have been reported to promote cognitive functions. Biotransformation of polyphenols is needed to obtain metabolites active in brain and it occurs through their processing by gut microbiota. Polyphenols metabolites could directly act as neurotransmitters crossing the blood-brain barrier or indirectly by modulating the cerebrovascular system. The microbiota-gut-brain axis is considered a neuroendocrine system that acts bidirectionally and plays an important role in stress responses. The metabolites produced by microbiota metabolism can modulate gut bacterial composition and brain biochemistry acting as neurotransmitters in the central nervous system. Gut microbiota composition can be influenced by dietary ingestion of natural bioactive molecules such as probiotics, prebiotics and polyphenol. Microbiota composition can be altered by dietary changes and gastrointestinal dysfunctions are observed in neurodegenerative diseases. In addition, several pieces of evidence support the idea that alterations in gut microbiota and enteric neuroimmune system could contribute to onset and progression of these age-related disorders. The impact of polyphenols on microbiota composition strengthens the idea that maintaining a healthy microbiome by modulating diet is essential for having a healthy brain across the lifespan. Moreover, it is emerging that they could be used as novel therapeutics to prevent brain from neurodegeneration.展开更多
Context: The gut microbiota represents a complex ecosystem encompassing all unicellular microorganisms residing in the digestive tract, primarily bacteria, fungi, archaea, and even viruses. The relationship between th...Context: The gut microbiota represents a complex ecosystem encompassing all unicellular microorganisms residing in the digestive tract, primarily bacteria, fungi, archaea, and even viruses. The relationship between the host and the microbiota is symbiotic: bacteria benefit from a stable environment, while the host gains numerous capabilities in terms of digestion, metabolism, nutrition, and immunity. However, numerous studies suggest that the gut microbiota plays a crucial role in various non-communicable diseases, including obesity, chronic inflammatory bowel diseases, allergic and immune disorders, behavioral disorders, and even certain cancers. The objective of our study was to characterize the gut microbiota of a group of breast cancer patients by comparing it to that of control subjects in Côte d’Ivoire, using a metagenomic approach. Method: A case-control study was conducted from May 2020 to September 2023. A total of 85 women (39 cases and 46 controls) were recruited, and stool samples were collected from both breast cancer patients and healthy women. Among these, ten (10) samples from patients and ten (10) samples from healthy women were randomly selected for the study of the gut microbiota. The gut microbiota was characterized by sequencing the V4 region of 16S rRNA using metagenomic NGS technology, and bioinformatic analysis was performed using the mothur pipeline. Results: In women with breast cancer, we observed a reduction in the relative abundance of the phyla Firmicutes and Bacteroidetes, as well as an increase in the phyla Actinobacteria and Verrucomicrobia. Additionally, their microbiota exhibited lower Chao1 and Sobs diversities compared to the control women (p < 0.05). Molecular variance analysis (AMOVA) revealed a significant difference between the case and control groups (p < 0.001). This study has highlighted a significant difference in the relative abundance of major phyla within the gut microbiota of cases compared to healthy controls. It will contribute to enriching African and global 展开更多
Seasonal variations in gut microbiota of small mammals and how they are influenced by environmental variables are relatively poorly understood.We sampled 162 wild plateau pikas(Ochotona curzoniae)in 4 seasons over 2 a...Seasonal variations in gut microbiota of small mammals and how they are influenced by environmental variables are relatively poorly understood.We sampled 162 wild plateau pikas(Ochotona curzoniae)in 4 seasons over 2 and a half years and recorded the air temperature,precipitation,and nutrient content in edible vegetation at the sampling site.After conducting 16S rRNA and shotgun metagenomic sequencing,we found that the highest alpha diversity,the relative abundance of Firmicutes,and the simplest co-occurrence network occurred in winter,whereas the highest relative abundance of Proteobacteria and the most complex network structure were observed in spring.The highest relative abundance of Verrucomicrobiota and Spirochaetota was seen in summer and autumn,respectively.Air temperature,precipitation,and the contents of crude protein,crude fiber,and polysaccharide in vegetation had significant effects on the seasonal changes in gut microbiota.Diet contributed more to microbial variation than climatic factors.Metagenomic analysis revealed that the amino acid metabolism pathway and axillary activity enzymes were most abundant in summer,while abundance of carbohydrate-binding modules and carbohydrate esterases was highest in spring.These microbial variations were related to the changes in dietary nutrition,indicating that gut microbiota of plateau pika contribute to the efficient use of food resources.This study provides new evidence of how external environmental factors affect the intestinal environment of small mammals.展开更多
Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils.However,little is known about the effects of plant-derived fertilizer on soil antibiotic resistome.Herein,metagenomic sequen...Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils.However,little is known about the effects of plant-derived fertilizer on soil antibiotic resistome.Herein,metagenomic sequencing was used to investigate the effects of a plantderived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes(ARGs)in a soybean field along crop growth stages.ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure.The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly(P<0.05)elevated at the sprout stage,to a level comparable to that in the manured soils.Whereas,unlike chicken manure mainly introducing manure-borne ARGs to soil,the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria.ARGs with abundances in amended soils significantly(P<0.05)higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs.Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest.Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer,while in manured soils were Firmicutes and Actinobacteria.As revealed by multivariate statistical analyses,variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients,which was different from the failed establishment of manure-borne bacteria in the manured soils.Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome,and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.展开更多
Next-generation sequencing （NGS） technology has revolutionized and significantly impacted metagenomic research.However,the NGS data usually contains sequencing artifacts such as low-quality reads and contaminating r...Next-generation sequencing （NGS） technology has revolutionized and significantly impacted metagenomic research.However,the NGS data usually contains sequencing artifacts such as low-quality reads and contaminating reads,which will significantly compromise downstream analysis.Many quality control （QC） tools have been proposed,however,few of them have been verified to be suitable or efficient for metagenomic data,which are composed of multiple genomes and are more complex than other kinds of NGS data.Here we present a metagenomic data QC method named Meta-QC-Chain.Meta-QC-Chain combines multiple QC functions： technical tests describe input data status and identify potential errors,quality trimming filters poor sequencing-quality bases and reads,and contamination screening identifies higher eukaryotic species,which are considered as contamination for metagenomic data.Most computing processes are optimized based on parallel programming.Testing on an 8-GB real dataset showed that Meta-QC-Chain trimmed low sequencing-quality reads and contaminating reads,and the whole quality control procedure was completed within 20 min.Therefore,Meta-QC-Chain provides a comprehensive,useful and high-performance QC tool for metagenomic data.Meta-QC-Chain is publicly available for free at： http：//computationalbioenergy.org/meta-qc-chain.html.展开更多
Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted...Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted. The illumina MiSeq sequencing was held and the diversity indices have been computed. Illumina MiSeq sequencing revealed 21 Phyla, four of which were abundant: Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. Soil microbial communities in the studied samples were phylogenetically diverse but with a stable community structure. 17 classes are represented with relative abundances of Rihzobiales, Bacillales, Actinomycetales and Acidobacteriales. 40 families, the Alphaproteobacteria, the Bacilli and the 12 Actinobacteria. 83 orders among which the Rhizobiales are the most abundant followed by Bacillales and the least abundant followed by the Flavobacteriaceae. Of the 28 genera listed, the Bradyrhizobium is the most dominant in Mw3 and Mw4. 25 listed species, Bradyrhizobium, Bacillus, Actinoplanes, and Candidatu coribacter Acidobacterium are the most abundant species. The Shannon indices of Mw3 and Mw4 are equal, the H’max of Mw4 is greater than the H’max of Mw3. The Simpson index of Mw4 is equal to the Simpson index of Mw3, and the Pielou index (J) of Mw4 is less than the R of Mw3, but very close. This study opens interesting perspectives on the knowledge and exploitation of telluric bacteria in several areas of life.展开更多
Background:For patients with lung cancer,timely identification of new lung lesions as infectious or non-infectious,and accurate identification of pathogens is very important in improving OS of patients.As a new auxiliar...Background:For patients with lung cancer,timely identification of new lung lesions as infectious or non-infectious,and accurate identification of pathogens is very important in improving OS of patients.As a new auxiliary examination,metagenomic next-generation sequencing(mNGS)is believed to be more accurate in diagnosing infectious diseases in patients without underlying diseases,compared with conventional microbial tests(CMTs).We designed this study tofind out whether mNGS has better performance in distinguishing infectious and non-infectious diseases in lung cancer patients using bronchoalveolar lavagefluid(BALF).Materials and Methods:This study was a real-world retrospective review based on electronic medical records of lung cancer patients with bronchoalveolar lavage(BAL)and BALF commercial mNGS testing as part of clinical care from 1 April 2019 through 30 April 2022 at The First Affiliated Hospital of Sun Yat-sen University.164 patients were included in this study.Patients were categorized into the pulmonary non-infectious disease(PNID)group(n=64)and the pulmonary infectious disease(PID)group(n=100)groups based onfinal diagnoses.Results:BALF mNGS increased the sensitivity rate by 60%compared to CMTs(81%vs.21%,p<0.05),whereas there was no significant difference in specificity(75%vs.98.4%,p>0.1).Among the patients with PID,bacteria were the most common cause of infection.Fungal infections occurred in 32%of patients,and Pneumocystis Yersini was most common.Patients with Tyrosine kinase inhibitors(TKIs)therapy possess longer overall survival(OS)than other anti-cancer agents,the difference between TKIs and immuno-checkpoint inhibitors(ICIs)was insignificant(median OS TKIs vs.ICIs vs.Anti-angiogenic vs.Chemo vs.Radiotherapy=76 vs.84 vs.61 vs.58 vs.60).Conclusions:our study indicates that BALF mNGS can add value by improving overall sensitivity in lung cancer patients with potential pulmonary infection,and was outstanding in identifying Pneumocystis infection.It could be able to help physicians adjust the 展开更多
基金supported by grants from Scienceand Technology Committee of Shanghai (18411951400)KeyClinical Medical Specialties Project in Shanghai Pudong NewArea (PWZzk2017-22)+1 种基金Science and Technology Action Plan(19495810200)Leading Talent Project in Shanghai Pudong NewArea Health System (PWRl2018-08).
文摘BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis patients.METHODS: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were recorded.The correlations between pathogen types and sepsis severity and survival rate were evaluated.RESULTS: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of sepsis.CONCLUSIONS: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.
基金Supported by National Natural Science Foundation of China(No.81473604)Natural Science Foundation of Zhejiang Province,China(No.LY19H270013)
文摘Objective: To explore the change of intestinal microecology in patients with primary Sjogren’s syndrome(p SS) and correlation with disease activity, and also discuss the therapy effect of Yangyin Yiqi Huoxue Recipe(养阴益气活血方, YYHD). Methods: Sixteen p SS patients were enrolled in the present study, who received 3-month treatment of YYHR, 200 mL orally twice daily. Their pre-and post-test ESSDAI scores, erythrocyte sedimentation rate(ESR) and serum immunoglobulin G(IgG) levels were measured respectively. The 16 Sr DNA metagenomic sequencing was used to detect and analyze the abundance and diversity of intestinal bacteria flora and the proportion of bacteria at the levels of phylum, family, and genus, in comparision with those of 6 healthy subjects in the control group. Results: The abundance and diversity of intestinal bacteria flora in pSS patients were lower than those of healthy subjects(P<0.05). After the treatment with YYHD, patients’ ESSDAI score and levels of IgG and ESR have decreased significantly(P<0.05). At the phylum level, the proportions of Actinobacteria, Firmicutes, Fusobacteria and Proteobacteria have reduced sharply, while the proportions of Bacteroidetes, Teneriquetes and Candidate-division-TM7 have increased significantly by treatment(all P<0.05). At the classification level, such treatment has caused a significant decrease in the proportions of Bacteroidaceae, Ruminococcaceae, Veillonellaceae, and Enterobacteriacea(all P<0.05), but a significant increase in the proportion of Lachnospiraceae(P<0.05). At the genus level, the treatment has significantly decreased the proportions of Bifidobacterium, Bacteroides, Escherichia-Shigella, Faecalibacterium and Prevotella(all P<0.05), but significantly increased the proportion of Clostridia(P<0.05), close to the levels of healthy subjects(P>0.05). Conclusions: There exists an imbalance of intestinal microecology in p SS patients, which can be improved through the treatment with YYHD. Besides, such treatment can also improve the disease ac
文摘BACKGROUND Chlamydia psittaci(C.psittaci)is a gram-negative intracellular parasitic pathogenic bacterium that can infect avian and mammalian hosts,including humans.The detection of C.psittaci infections typically relies on traditional antigen-based immunoassays or serological testing that often lack sensitivity and/or specificity.Metagenomic next generation sequencing(mNGS)is an emerging tool for diagnosis.AIM To demonstrate that mNGS represents a valuable tool for rapid,sensitive,and accurate pathogen detection including C.psittaci infections.METHODS Four cases of psittacosis pneumonia and one case of pediatric psittacosis meningitis were diagnosed between December 2019 and May 2020 using mNGS at Changzhou Second People’s Hospital affiliated to Nanjing Medical University.Patients’clinical characteristics,manifestations,and treatment histories were retrospectively evaluated.RESULTS All five patients had a history of exposure to wild(psittacine or other birds)or domesticated birds(chickens).All patients had a high fever(>39℃)and three of them(60%)experienced organ insufficiency during the disease.The laboratory data showed normal to slightly increased leucocyte and neutrophil counts,and elevated procalcitonin levels in all five cases,and very high C-reactive protein levels in psittacosis pneumonia patients.mNGS identified a potential pathogen,C.psittaci,in patients’bronchoalveolar lavage fluid or cerebrospinal fluid.Computed tomography revealed lung air-space consolidation,pleural thickening,and effusion fluid buildup in psittacosis pneumonia cases,and an arachnoid cyst in the right temporal lobe of the pediatric psittacosis meningitis patient.All patients experienced complete recovery following the administration of targeted antichlamydia therapy.CONCLUSION This study not only demonstrated that mNGS represents a valuable tool for rapid,sensitive,and accurate pathogen detection,but also raised public health concerns over C.psittaci infections.
基金supported by Italian Ministry of Health ‘‘Ricerca Corrente”(to SF)
文摘Increasing evidence suggests that food ingested polyphenols can have beneficial effects in neuronal protection acting against oxidative stress and inflammatory injury. Moreover, polyphenols have been reported to promote cognitive functions. Biotransformation of polyphenols is needed to obtain metabolites active in brain and it occurs through their processing by gut microbiota. Polyphenols metabolites could directly act as neurotransmitters crossing the blood-brain barrier or indirectly by modulating the cerebrovascular system. The microbiota-gut-brain axis is considered a neuroendocrine system that acts bidirectionally and plays an important role in stress responses. The metabolites produced by microbiota metabolism can modulate gut bacterial composition and brain biochemistry acting as neurotransmitters in the central nervous system. Gut microbiota composition can be influenced by dietary ingestion of natural bioactive molecules such as probiotics, prebiotics and polyphenol. Microbiota composition can be altered by dietary changes and gastrointestinal dysfunctions are observed in neurodegenerative diseases. In addition, several pieces of evidence support the idea that alterations in gut microbiota and enteric neuroimmune system could contribute to onset and progression of these age-related disorders. The impact of polyphenols on microbiota composition strengthens the idea that maintaining a healthy microbiome by modulating diet is essential for having a healthy brain across the lifespan. Moreover, it is emerging that they could be used as novel therapeutics to prevent brain from neurodegeneration.
文摘Context: The gut microbiota represents a complex ecosystem encompassing all unicellular microorganisms residing in the digestive tract, primarily bacteria, fungi, archaea, and even viruses. The relationship between the host and the microbiota is symbiotic: bacteria benefit from a stable environment, while the host gains numerous capabilities in terms of digestion, metabolism, nutrition, and immunity. However, numerous studies suggest that the gut microbiota plays a crucial role in various non-communicable diseases, including obesity, chronic inflammatory bowel diseases, allergic and immune disorders, behavioral disorders, and even certain cancers. The objective of our study was to characterize the gut microbiota of a group of breast cancer patients by comparing it to that of control subjects in Côte d’Ivoire, using a metagenomic approach. Method: A case-control study was conducted from May 2020 to September 2023. A total of 85 women (39 cases and 46 controls) were recruited, and stool samples were collected from both breast cancer patients and healthy women. Among these, ten (10) samples from patients and ten (10) samples from healthy women were randomly selected for the study of the gut microbiota. The gut microbiota was characterized by sequencing the V4 region of 16S rRNA using metagenomic NGS technology, and bioinformatic analysis was performed using the mothur pipeline. Results: In women with breast cancer, we observed a reduction in the relative abundance of the phyla Firmicutes and Bacteroidetes, as well as an increase in the phyla Actinobacteria and Verrucomicrobia. Additionally, their microbiota exhibited lower Chao1 and Sobs diversities compared to the control women (p < 0.05). Molecular variance analysis (AMOVA) revealed a significant difference between the case and control groups (p < 0.001). This study has highlighted a significant difference in the relative abundance of major phyla within the gut microbiota of cases compared to healthy controls. It will contribute to enriching African and global
基金supported by the Grant from CAS No.152111KYSB20160089Qinghai innovation platform construction project by Chinese Academy of Sciences(2021-ZJ-Y01)+2 种基金the project of western light for interdisciplinary teamScience and Technology Department of Qinghai Province Major Project“Sanjiangyaun National Park Animal Genome Program”the Natural Science Foundation of Qinghai Province(2019-ZJ-7024).
文摘Seasonal variations in gut microbiota of small mammals and how they are influenced by environmental variables are relatively poorly understood.We sampled 162 wild plateau pikas(Ochotona curzoniae)in 4 seasons over 2 and a half years and recorded the air temperature,precipitation,and nutrient content in edible vegetation at the sampling site.After conducting 16S rRNA and shotgun metagenomic sequencing,we found that the highest alpha diversity,the relative abundance of Firmicutes,and the simplest co-occurrence network occurred in winter,whereas the highest relative abundance of Proteobacteria and the most complex network structure were observed in spring.The highest relative abundance of Verrucomicrobiota and Spirochaetota was seen in summer and autumn,respectively.Air temperature,precipitation,and the contents of crude protein,crude fiber,and polysaccharide in vegetation had significant effects on the seasonal changes in gut microbiota.Diet contributed more to microbial variation than climatic factors.Metagenomic analysis revealed that the amino acid metabolism pathway and axillary activity enzymes were most abundant in summer,while abundance of carbohydrate-binding modules and carbohydrate esterases was highest in spring.These microbial variations were related to the changes in dietary nutrition,indicating that gut microbiota of plateau pika contribute to the efficient use of food resources.This study provides new evidence of how external environmental factors affect the intestinal environment of small mammals.
基金supported by the National Natural Science Foundation of China (Nos.32141002 and 22076203)。
文摘Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils.However,little is known about the effects of plant-derived fertilizer on soil antibiotic resistome.Herein,metagenomic sequencing was used to investigate the effects of a plantderived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes(ARGs)in a soybean field along crop growth stages.ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure.The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly(P<0.05)elevated at the sprout stage,to a level comparable to that in the manured soils.Whereas,unlike chicken manure mainly introducing manure-borne ARGs to soil,the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria.ARGs with abundances in amended soils significantly(P<0.05)higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs.Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest.Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer,while in manured soils were Firmicutes and Actinobacteria.As revealed by multivariate statistical analyses,variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients,which was different from the failed establishment of manure-borne bacteria in the manured soils.Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome,and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.
基金supported by the National High-tech R&D Program(863 Program Grant Nos.2009AA02Z310 and 2012AA02A707)funded by Ministry of Science and Technology of China+1 种基金Natural Science Foundation of China(Grant Nos.61103167 and 31271410)Chinesisch-Deutschen Zentrum für Wissenschaftsfrderung(Grant No.GZ 878)
文摘Next-generation sequencing （NGS） technology has revolutionized and significantly impacted metagenomic research.However,the NGS data usually contains sequencing artifacts such as low-quality reads and contaminating reads,which will significantly compromise downstream analysis.Many quality control （QC） tools have been proposed,however,few of them have been verified to be suitable or efficient for metagenomic data,which are composed of multiple genomes and are more complex than other kinds of NGS data.Here we present a metagenomic data QC method named Meta-QC-Chain.Meta-QC-Chain combines multiple QC functions： technical tests describe input data status and identify potential errors,quality trimming filters poor sequencing-quality bases and reads,and contamination screening identifies higher eukaryotic species,which are considered as contamination for metagenomic data.Most computing processes are optimized based on parallel programming.Testing on an 8-GB real dataset showed that Meta-QC-Chain trimmed low sequencing-quality reads and contaminating reads,and the whole quality control procedure was completed within 20 min.Therefore,Meta-QC-Chain provides a comprehensive,useful and high-performance QC tool for metagenomic data.Meta-QC-Chain is publicly available for free at： http：//computationalbioenergy.org/meta-qc-chain.html.
文摘Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted. The illumina MiSeq sequencing was held and the diversity indices have been computed. Illumina MiSeq sequencing revealed 21 Phyla, four of which were abundant: Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. Soil microbial communities in the studied samples were phylogenetically diverse but with a stable community structure. 17 classes are represented with relative abundances of Rihzobiales, Bacillales, Actinomycetales and Acidobacteriales. 40 families, the Alphaproteobacteria, the Bacilli and the 12 Actinobacteria. 83 orders among which the Rhizobiales are the most abundant followed by Bacillales and the least abundant followed by the Flavobacteriaceae. Of the 28 genera listed, the Bradyrhizobium is the most dominant in Mw3 and Mw4. 25 listed species, Bradyrhizobium, Bacillus, Actinoplanes, and Candidatu coribacter Acidobacterium are the most abundant species. The Shannon indices of Mw3 and Mw4 are equal, the H’max of Mw4 is greater than the H’max of Mw3. The Simpson index of Mw4 is equal to the Simpson index of Mw3, and the Pielou index (J) of Mw4 is less than the R of Mw3, but very close. This study opens interesting perspectives on the knowledge and exploitation of telluric bacteria in several areas of life.
基金This study was funded by Science and Technology Projects in Guangzhou(No.202002030023).
文摘Background:For patients with lung cancer,timely identification of new lung lesions as infectious or non-infectious,and accurate identification of pathogens is very important in improving OS of patients.As a new auxiliary examination,metagenomic next-generation sequencing(mNGS)is believed to be more accurate in diagnosing infectious diseases in patients without underlying diseases,compared with conventional microbial tests(CMTs).We designed this study tofind out whether mNGS has better performance in distinguishing infectious and non-infectious diseases in lung cancer patients using bronchoalveolar lavagefluid(BALF).Materials and Methods:This study was a real-world retrospective review based on electronic medical records of lung cancer patients with bronchoalveolar lavage(BAL)and BALF commercial mNGS testing as part of clinical care from 1 April 2019 through 30 April 2022 at The First Affiliated Hospital of Sun Yat-sen University.164 patients were included in this study.Patients were categorized into the pulmonary non-infectious disease(PNID)group(n=64)and the pulmonary infectious disease(PID)group(n=100)groups based onfinal diagnoses.Results:BALF mNGS increased the sensitivity rate by 60%compared to CMTs(81%vs.21%,p<0.05),whereas there was no significant difference in specificity(75%vs.98.4%,p>0.1).Among the patients with PID,bacteria were the most common cause of infection.Fungal infections occurred in 32%of patients,and Pneumocystis Yersini was most common.Patients with Tyrosine kinase inhibitors(TKIs)therapy possess longer overall survival(OS)than other anti-cancer agents,the difference between TKIs and immuno-checkpoint inhibitors(ICIs)was insignificant(median OS TKIs vs.ICIs vs.Anti-angiogenic vs.Chemo vs.Radiotherapy=76 vs.84 vs.61 vs.58 vs.60).Conclusions:our study indicates that BALF mNGS can add value by improving overall sensitivity in lung cancer patients with potential pulmonary infection,and was outstanding in identifying Pneumocystis infection.It could be able to help physicians adjust the
