The microbial synthesis of sulfonolipids within the human body is likely involved in maintaining human health or causing diseases.However,the enzymes responsible for their biosynthesis remain largely unknown.In this s...The microbial synthesis of sulfonolipids within the human body is likely involved in maintaining human health or causing diseases.However,the enzymes responsible for their biosynthesis remain largely unknown.In this study,we identified and verified the role of 3-ketocapnine reductase,the third-step enzyme,in the four-step conversion of L-phosphoserine into sulfobacin B both in vivo and in vitro.This finding builds upon our previous research into sulfonolipid biosynthesis,which focused on the vaginal bacterium Chryseobacterium gleum DSM 16776 and the gut bacterium Alistipes finegoldii DSM 17242.Through comprehensive gene mapping,we demonstrate the widespread presence of potential sulfonolipid biosynthetic genes across diverse bacterial species inhabiting various regions of the human body.These findings shed light on the prevalence of sulfonolipid-like metabolites within the human microbiota,suggesting a potential role for these lipid molecules in influencing the intricate biointeractions within the complex microbial ecosystem of the human body.展开更多
Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genome...Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota".Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood–Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.展开更多
On May 21,2021,a local case of coronavirus disease 2019(COVID-19)was confirmed in a 75-year-old woman(experienced onset of symptoms on May 18)in Liwan District,Guangzhou City,Guangdong Province,China.The number of inf...On May 21,2021,a local case of coronavirus disease 2019(COVID-19)was confirmed in a 75-year-old woman(experienced onset of symptoms on May 18)in Liwan District,Guangzhou City,Guangdong Province,China.The number of infections has increased in the following 10 days and led to 5 generations of transmission.展开更多
Theionarchaea is a recently described archaeal class within the Euryarchaeota.While it is widely distributed in sediment ecosystems,little is known about its metabolic potential and ecological features.Here,we used me...Theionarchaea is a recently described archaeal class within the Euryarchaeota.While it is widely distributed in sediment ecosystems,little is known about its metabolic potential and ecological features.Here,we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes,which were further divided into two subgroups,from coastal mangrove sediments of China and seawater columns of the Yap Trench.Genomic analysis revealed that apart from the canonical sulfhydrogenase,Theionarchaea harbor genes encoding heliorhodopsin,group 4[NiFe]-hydrogenase,and flagellin,in which genes for heliorhodopsin and group 4[NiFe]-hydrogenase were transcribed in mangrove sediment.Further,the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics,and the potential carbon substrates include detrital proteins,hemicellulose,ethanol,and CO_(2).The genes for organic substrate metabolism(mainly detrital protein and amino acid metabolism genes)have relatively higher transcripts in the top sediment layers in mangrove wetlands.In addition,co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters(e.g.,Chloroflexi)and methanogens.Collectively,these observations expand the current knowledge of the metabolic potential of Theionarchaea,and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.展开更多
Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance.Here,we retrieved 11 metagenomic-assembled genomes(MAGs)a...Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance.Here,we retrieved 11 metagenomic-assembled genomes(MAGs)affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench.Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum,subsequently named Candidatus Qinglongiota,Candidatus Heilongiota,and Candidatus Canglongiota.Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle,with the potential to utilize various types of sugars,proteins,and/or short-chain fatty acids through anaerobic pathways.This was further confirmed by a global distribution map of the three phyla,indicating a preference for oxygen-limited or particle-attached niches,such as anoxic sedimentary environments.Of note,Candidatus Canglongiota genomes harbor genes for the complete WoodLjungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria.Evolutionary analysis indicated that gene gain and loss events,and horizontal gene transfer(HGT)play important roles in shaping the genomic and metabolic features of the three new phyla.This study presents the genomic insight into the ecology,metabolism,and evolution of three new phyla,which broadens the phylum-level diversity within the domain Bacteria.展开更多
基金supported by the Shenzhen Bay Laboratory Startup Funds(21230051 to X.T.)Guangdong Province's Pearl River Recruitment Program of Talents(2021QN02Y855 to X.T.)+2 种基金GuangDong Basic and Applied Basic Research Foundation(2021A1515110334 to M.C.)the Natural Science Basic Research Plan in Shaanxi Province of China(2023-JC-QN-0160 to L.H.)the Scientific Research Foundation of Northwest A&F University(Z1090122052 to L.H.).
文摘The microbial synthesis of sulfonolipids within the human body is likely involved in maintaining human health or causing diseases.However,the enzymes responsible for their biosynthesis remain largely unknown.In this study,we identified and verified the role of 3-ketocapnine reductase,the third-step enzyme,in the four-step conversion of L-phosphoserine into sulfobacin B both in vivo and in vitro.This finding builds upon our previous research into sulfonolipid biosynthesis,which focused on the vaginal bacterium Chryseobacterium gleum DSM 16776 and the gut bacterium Alistipes finegoldii DSM 17242.Through comprehensive gene mapping,we demonstrate the widespread presence of potential sulfonolipid biosynthetic genes across diverse bacterial species inhabiting various regions of the human body.These findings shed light on the prevalence of sulfonolipid-like metabolites within the human microbiota,suggesting a potential role for these lipid molecules in influencing the intricate biointeractions within the complex microbial ecosystem of the human body.
基金the National Natural Science Foundation of China (91851105, 31622002, 31970105, 31600093, and 31700430)the Shenzhen Science and Technology Program (JCYJ20170818091727570 and KQTD20180412181334790)+3 种基金the Key Project of Department of Education of Guangdong Province (2017KZDXM071)the China Postdoctoral Science Foundation (2018M633111)the DFG (Deutsche Forschungsgemeinschaft) Cluster of Excellence EXC 309 “The Ocean in the Earth System - MARUM - Center for Marine Environmental Sciences” (project ID 49926684)the University of Bremen。
文摘Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota".Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involved in the tetrahydromethanopterin-based Wood–Ljungdahl pathway. Transcriptomics showed that most of our identified Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, occupying ecological niches in different depths of layers of the sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.
基金The Key-Area Research and Development Program of Guangdong Province(2019B111103001,2020B111107001)The National Natural Science Foundation of China(No.82041030).
文摘On May 21,2021,a local case of coronavirus disease 2019(COVID-19)was confirmed in a 75-year-old woman(experienced onset of symptoms on May 18)in Liwan District,Guangzhou City,Guangdong Province,China.The number of infections has increased in the following 10 days and led to 5 generations of transmission.
基金supported by the National Natural Science Foundation of China(91851105,31970105,31600093,3170043091951102)+1 种基金the Innovation Team Project of Universities in Guangdong Province(2020KCXTD023)the Shenzhen Science and Technology Program(JCYJ20200109105010363,JCYJ20180305163524811 and JCYJ20190808152403587)。
文摘Theionarchaea is a recently described archaeal class within the Euryarchaeota.While it is widely distributed in sediment ecosystems,little is known about its metabolic potential and ecological features.Here,we used metagenomics and metatranscriptomics to characterize 12 theionarchaeal metagenome-assembled genomes,which were further divided into two subgroups,from coastal mangrove sediments of China and seawater columns of the Yap Trench.Genomic analysis revealed that apart from the canonical sulfhydrogenase,Theionarchaea harbor genes encoding heliorhodopsin,group 4[NiFe]-hydrogenase,and flagellin,in which genes for heliorhodopsin and group 4[NiFe]-hydrogenase were transcribed in mangrove sediment.Further,the theionarchaeal substrate spectrum may be broader than previously reported as revealed by metagenomics and metatranscriptomics,and the potential carbon substrates include detrital proteins,hemicellulose,ethanol,and CO_(2).The genes for organic substrate metabolism(mainly detrital protein and amino acid metabolism genes)have relatively higher transcripts in the top sediment layers in mangrove wetlands.In addition,co-occurrence analysis suggested that the degradation of these organic compounds by Theionarchaea might be processed in syntrophy with fermenters(e.g.,Chloroflexi)and methanogens.Collectively,these observations expand the current knowledge of the metabolic potential of Theionarchaea,and shed light on the metabolic strategies and roles of these archaea in the marine ecosystems.
基金supported by the National Natural Science Foundation of China(91951102,31800105,31970105,32061133009)the Innovation Team Project of Universities in Guangdong Province(2020KCXTD023)+1 种基金the Scientific Research Foundation of Third Institute of Oceanography,MNR(2019022)the Science and Technology Innovation Committee of Shenzhen(JCYJ20190808152403587,JCYJ20180305163524811,JCYJ20200109105010363)。
文摘Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance.Here,we retrieved 11 metagenomic-assembled genomes(MAGs)affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench.Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum,subsequently named Candidatus Qinglongiota,Candidatus Heilongiota,and Candidatus Canglongiota.Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle,with the potential to utilize various types of sugars,proteins,and/or short-chain fatty acids through anaerobic pathways.This was further confirmed by a global distribution map of the three phyla,indicating a preference for oxygen-limited or particle-attached niches,such as anoxic sedimentary environments.Of note,Candidatus Canglongiota genomes harbor genes for the complete WoodLjungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria.Evolutionary analysis indicated that gene gain and loss events,and horizontal gene transfer(HGT)play important roles in shaping the genomic and metabolic features of the three new phyla.This study presents the genomic insight into the ecology,metabolism,and evolution of three new phyla,which broadens the phylum-level diversity within the domain Bacteria.
