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metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process:From collapse to recovery

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Journal of Environmental Sciences 2024年第1期135卷 210-221页

作者： Hong Wang Hui Gong Xiaohu Dai Min Yang State Key Laboratory of Pollution Control and Resource Reuse College of Environmental Science and EngineeringTongji UniversityShanghai 200092China BIOMATH Department of Data Analysis and Mathematical ModellingGhent UniversityGhent 9000Belgium

Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.

关键词： Partial nitritation-anammox metagenomics Microbial community Functional metabolism Recovery

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Correlation between the gut microbiome and neurodegenerative diseases:a review of metagenomics evidence

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Neural Regeneration Research 2024年第4期19卷 833-845页

作者： Xiaoyan Liu Yi Liu Junlin Liu Hantao Zhang Chaofan Shan Yinglu Guo Xun Gong Mengmeng Cui Xiubin Li Min Tang School of Life Sciences Jiangsu University Institute of Animal Husbandry Jiangsu Academy of Agricultural Sciences Department of Rheumatology&Immunology Affiliated Hospital of Jiangsu University Department of Neurology The Second Affiliated Hospital of Shandong First Medical University

A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis.As a contributing factor,microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases,such as Alzheimer’s disease,Parkinson’s disease,and amyotrophic lateral sclerosis.High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota’s diverse microorganisms,and for both neuroimmune and neuroendocrine systems.Here,we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases,with an emphasis on multi-omics studies and the gut virome.The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated.Finally,we discuss the role of diet,prebiotics,probiotics,postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.

关键词： biomarker diet pattern gut microbiota gut-brain axis metagenomics mitochondrial dysfunction multi-omics neurodegenerative disease neuroinflammation probiotic

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Recent advances in the culture-independent discovery of natural products using metagenomic approaches

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Chinese Journal of Natural Medicines 2024年第2期22卷 100-111页

作者： SHEN Yiping LIU Nan WANG Zongqiang Laboratory of Microbial Drug Discovery China Pharmaceutical UniversityNanjing 211198China

Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads.However,the cultivation of only about 1%of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria.Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods.This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening,sequence tag-based homology screening,and bioinformatic-assisted chemical synthesis.Through this process,numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories.This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.

关键词： metagenomics Culture-independent approach Natural product Functional screening Sequence tag-based homology screening Syn-BNP

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Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones

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Journal of Animal Science and Biotechnology 2024年第2期15卷 578-599页

作者： Min Liu Jia Zhang Yunyan Zhou Shuqi Xiong Mengqing Zhou Lin Wu Qin Liu Zhe Chen Hui Jiang Jiawen Yang Yuxin Liu Yaxiang Wang Congying Chen Lusheng Huang National Key Laboratory of Swine Genetic Improvement and Germplasm Innovation Jiangxi Agricultural UniversityNanchang 330045China

Background Sex hormones play important roles in the estrus return of post-weaning sows.Previous studies have demonstrated a complex and bi-directional regulation between sex hormones and gut microbiota.However,the extent to which the gut microbiota affects estrus return of post-weaning sows is largely unknown.Results In this study,we first screened 207 fecal samples from well-phenotyped sows by 16S rRNA gene sequencing and identified significant associations between microbes and estrus return of post-weaning sows.Using metagenomic sequencing data from 85 fecal samples,we identified 37 bacterial species that were significantly associated with estrus return.Normally returning sows were characterized by increased abundances of L.reuteri and P.copri and decreased abundances of B.fragilis,S.suis,and B.pseudolongum.The changes in gut microbial composition significantly altered the functional capacity of steroid hormone biosynthesis in the gut microbiome.The results were confirmed in a validation cohort.Significant changes in sex steroid hormones and related compounds were found between normal and non-return sows via metabolome analysis.An integrated analysis of differential bacterial species,metagenome,and fecal metabolome provided evidence that normal return-associated bacterial species L.reuteri and Prevotella spp.participated in the degradation of pregnenolone,progesterone,and testosterone,thereby promoting estrogen biosynthesis.Furthermore,the microbial metabolites related to sow energy and nutrient supply or metabolic disorders also showed relationships with sow estrus return.Conclusions An integrated analysis of differentially abundant bacterial species,metagenome,and fecal metabolome revealed the involvement of L.reuteri and Prevotella spp.in sow estrus return.These findings provide deep insight into the role of gut microbiota in the estrus return of post-weaning sows and the complex cross-talk between gut microbiota and sex hormones,suggesting that the manipulation of the gut microbiota could be an effective st

关键词： Estrus return Fecal metabolome Gut microbiota metagenomics Sex steroid hormones Sow

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Soil bacterial and fungal communities resilience to long-term nitrogen addition in subtropical forests in China

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Journal of Forestry Research 2024年第2期35卷 95-108页

作者： Xinlei Fu Yunze Dai Jun Cui Pengfei Deng Wei Fan Xiaoniu Xu School of Forestry and Landscape Architecture Anhui Agricultural UniversityHefei 230036AnhuiPeople’s Republic of China Suzhou Polytechnic Institute of Agriculture Suzhou 215008JiangsuPeople’s Republic of China College of Life and Environment Sciences Huangshan UniversityHuangshan 245041AnhuiPeople’s Republic of China

Atmospheric nitrogen(N)deposition is predicted to increase,especially in the subtropics.However,the responses of soil microorganisms to long-term N addition at the molecular level in N-rich subtropical forests have not been clarified.A long-term nutrient addition experiment was conducted in a subtropical evergreen old-growth forest in China.The four treatments were:control,low N(50 kg N ha^(-1)a^(-1)),high N(100 kg N ha^(-1)a^(-1)),and combined N and phosphorus(P)(100 kg N ha^(-1)a^(-1)+50 kg P ha^(-1)a^(-1)).Metagenomic sequencing characterized diversity and composition of soil microbial communities and used to construct bacterial/fungal co-occurrence networks.Nutrient-treated soils were more acidic and had higher levels of dissolved organic carbon than controls.There were no significant differences in microbial diversity and community composition across treatments.The addition of nutrients increased the abundance of copiotrophic bacteria and potentially beneficial microorganisms(e.g.,Gemmatimonadetes,Chaetomium,and Aureobasidium).Low N addition increased microbiome network connectivity.Three rare fungi were identified as module hubs under nutrient addition,indicating that low abundance fungi were more sensitive to increased nutrients.The results indicate that the overall composition of microbial communities was stable but not static to long-term N addition.Our findings provide new insights that can aid predictions of the response of soil microbial communities to long-term N addition.

关键词： Long-term nitrogen addition Old-growth subtropical forest metagenomics Beneficial microorganisms Co-occurrence network

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metagenomics reveals contrasting energy utilization efficiencies of captive and wild camels(Camelus ferus)

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Integrative Zoology 2022年第3期17卷 333-345页

作者： Liping YAN Liping TANG Zhichao ZHOU Wei LU Bo WANG Zhicheng SUN Xue JIANG Defu HU Junqing LI Dong ZHANG School of Ecology and Nature Conservation Beijing Forestry UniversityBeijingChina Gansu Endangered Animals Protection Center WuweiChina Administrative Bureau of Dunhuang Xihu National Nature Reserve DunhuangChina

Captive conditions can affect the symbiotic microbiome of animals.In this study,we compared the structural and functional differences of the gastrointestinal microbiomes of wild Bactrian camels(Camelus ferus)between wild and captive populations,as well as their different host energy utilization performances through metagenomics.The results showed that wild-living camels harbored more microbial taxa related to the production of volatile fatty acids,fewer methanogens,and fewer genes encoding enzymes involved in methanogenesis,leading to higher energy utilization efficiency compared to that of captive-living camels.These findings suggest that the wild-living camel fecal microbiome demonstrates a series of adaptive characteristics that enable the host to adjust to a relatively barren field environment.Our study provides novel insights into the mechanisms of wildlife adaptations to habitats from the perspective of the microbiome.

关键词： adaptability energy utilization gastrointestinal microbiome metagenomics wild and captive wild Bactrian camel

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Omics approaches in asthma research:Challenges and opportunities

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Chinese Medical Journal Pulmonary and Critical Care Medicine 2024年第1期2卷 1-9页

作者： Molin Yue Shiyue Tao Kristina Gaietto Wei Chen Department of Biostatistics School of Public HealthUniversity of PittsburghPittsburghPA 15224USA Division of Pediatric Pulmonary Medicine UPMC Children’s Hospital of PittsburghUniversity of PittsburghPittsburghPA 15224USA

Asthma,a chronic respiratory disease with a global prevalence of approximately 300 million individuals,presents a significant societal and economic burden.This multifaceted syndrome exhibits diverse clinical phenotypes and pathogenic endotypes influenced by various factors.The advent of omics technologies has revolutionized asthma research by delving into the molecular foundation of the disease to unravel its underlying mechanisms.Omics technologies are employed to systematically screen for potential biomarkers,encompassing genes,transcripts,methylation sites,proteins,and even the microbiome components.This review provides an insightful overview of omics applications in asthma research,with a special emphasis on genetics,transcriptomics,epigenomics,and the microbiome.We explore the cutting-edge methods,discoveries,challenges,and potential future directions in the realm of asthma omics research.By integrating multi-omics and non-omics data through advanced sta-tistical techniques,we aspire to advance precision medicine in asthma,guiding diagnosis,risk assessment,and personalized treatment strategies for this heterogeneous condition.

关键词： Asthma Genomics Transcriptomics Epigenomics metagenomics Multi-omics integration

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揭示氨对正己酸生产影响的机制——影响途径、关键酶和微生物

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Engineering 2024年第4期35卷 180-190页

作者： Qing-Lian Wu Ke-Xin Yuan Wei-Tong Ren Lin Deng Hua-Zhe Wang Xiao-Chi Feng He-Shan Zheng Nan-Qi Ren Wan-Qian Guo State Key Laboratory of Urban Water Resource and Environment Harbin Institute of TechnologyHarbin 150090China College of Architecture and Environment Sichuan UniversityChengdu 610065China State Key Laboratory of Urban Water Resource and Environment School of Civil and Environmental EngineeringHarbin Institute of Technology(Shenzhen)Shenzhen 518055China College of Chemistry and Chemical Engineering Qiqihar UniversityQiqihar 161006China

n-Caproate,which is produced via chain elongation(CE)using waste biomass,can supply various fossilderived products,thus advancing the realization of carbon neutrality.Ammonia released from the degradation of nitrogen-rich waste biomass can act as a nutrient or an inhibitor in anaerobic bioprocesses,including CE,with the distinction being primarily dependent on its concentration.Currently,the optimal concentration of ammonia and the threshold of toxicity for open-culture n-caproate production using ethanol as an electron donor,along with the underlying mechanisms,remain unclear.This study revealed that the optimal concentration of ammonia for n-caproate production was 2.0 g∙L^(-1),whereas concentrations exceeding this threshold markedly suppressed the CE performance.Exploration of the mechanism revealed the involvement of two forms of ammonia(i.e.,ammonium ions and free ammonia)in this inhibitory behavior.High ammonia levels(5.0 g∙L^(-1))induced excessive ethanol oxidation and suppressed the reverse b-oxidation(RBO)process,directly leading to the enhanced activities of enzymes(phosphotransacetylase and acetate kinase)responsible for acetate formation and diminished activities of butyryl-coenzyme A(CoA):acetyl-CoA transferase,caproyl-CoA:butyryl-CoA transferase,and caproyl-CoA:acetyl-CoA transferase that are involved in the syntheses of n-butyrate and n-caproate.Furthermore,the composition of the microbial community shifted from Paraclostridium dominance(at 0.1 g∙L^(-1)ammonia)to a co-dominance of Fermentimonas,Clostridium sensu stricto 12,and Clostridium sensu stricto 15 at 2.0 g∙L^(-1)ammonia.However,these CE-functional bacteria were mostly absent in the presence of excessive ammonia(5.0 g∙L^(-1)ammonia).Metagenomic analysis revealed the upregulation of functions such as RBO,fatty acid synthesis,K^(+)efflux,adenosine triphosphatase(ATPase)metabolism,and metal cation export in the presence of 2.0 g∙L^(-1)ammonia,collectively contributing to enhanced n-caproate production.Conversely,the aforementioned functions(exc

关键词： Ammonia inhibition Medium chain fatty acids n-Caproate Enzyme metagenomics

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metagenomics COMBINED WITH HIGHTHROUGHPUT SEQUENCING REVEALS THE METHANOGENIC POTENTIAL OF FRESH CORN STRAW UNDER THERMOPHILIC AND HIGH OLR

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Frontiers of Agricultural Science and Engineering 2023年第3期10卷 403-423页

作者： Jinzhi HUANG Xiaoting YAN Zhen LIU Mengyi WANG Yangyang HU Zhenyu LI Minsong LIN Yiqing YAO College of Mechanical and Electronic Engineering Northwest A&F UniversityYangling 712100China School of Ecology and Environment Northwestern Polytechnical UniversityXi’an 710072China College of Food Science and Engineering Northwest A&F UniversityYangling 712100China Chinese Academy for Environmental Planning Ministry of Ecology and Environment of the People’s Republic of ChinaBeijing 100012China Northwest Research Center of Rural Renewable Energy Exploitation and Utilization of Ministry of AgricultureNorthwest A&F UniversityYangling 712100China

Dry corn straw(DCS)is usually used in anaerobic digestion(AD),but fresh corn straw(FCS)has been given less consideration.In this study,the thermophilic AD of single-substrate(FCS and DCS)and co-digestion(straw with cattle manure)were investigated.The results show that when FCS was used as the single-substrate for AD,the methane production was 144 mL·g^(−1)·VS^(−1),which was 7.5%and 19.6%higher than that of single DCS and FCS with cattle manure,respectively.In addition,the structure of FCS was loose and coarse,which was easier to be degraded than DCS.At the hydrolysis and acidification stages,Clostridium_sensu_stricto_1,Clostridium_sensu_stricto_7 and Sporosarcina promoted the decomposition of organic matter,leading to volatile fatty acids(VFAs)accumulation.Methanosarcina(54.4%)activated multifunctional methanogenic pathways to avoid the VFAs inhibition,which was important at the CH_(4) production stage.The main pathway was hydrogenotrophic methanogenesis,with genes encoding formylmethanofuran dehydrogenase(K00200-K00203)and tetrahydromethanopterin Smethyltransferase(K00577-K00584).Methanosarcina also activated acetotrophic and methylotrophic methanogenesis pathways,with genes encoding acetyl phosphate(K13788)and methyl-coenzyme M reductase(K04480,K14080 and K14081),respectively.In the co-digestion,the methanogenic potential of FCS was also confirmed.This provides a scientific basis for regulating AD of crop straw.

关键词： fresh corn straw high solid anaerobic digestion metagenomics microbial communities thermophilic

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Diagnostic value of metagenomics next-generation sequencing technology in disseminated strongyloidiasis

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World Journal of Clinical Cases 2022年第33期10卷 12455-12457页

作者： Peng Song Xia Li Department of Respiratory Medicine Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250000Shandong ProvinceChina Department of Thoracic Surgery Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinan 250021Shandong ProvinceChina

The symptoms of disseminated strongyloidiasis are not typical,and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas.We report a 70-year-old woman who was diagnosed with Guillain-Barrésyndrome due to autonomic disturbance,symmetrical bulbar palsy,and lower-motor-nerve damage in the extremities;her symptoms continued to worsen after hormone and immunoglobulin therapy.Later,parasitic larvae were found in the patient’s gastric fluid,and metagenomic next generation sequencing(mNGS)detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms.The patient was diagnosed with disseminated strongyloidiasis.The patient was given albendazole for anthelmintic treatment,but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden.In recent years,mNGS has been increasingly used in clinical practice,and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas.Especially during the corona virus disease 2019 pandemic,mNGS technology has irreplaceable value in identifying the source of infection.

关键词： metagenomics Next-generation sequencing Disseminated Strongyloidiasis

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