Why and how to use the SeqCode

The SeqCode,formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data,is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species.While similar to the International Code of Nomenclature of Prokaryotes(ICNP)in structure and rules of priority,it does not require the deposition of type strains in international culture collections.Thus,it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections.Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes,the SeqCode is the only code suitable for naming the majority of prokaryotic species.The start date of the SeqCode was January 1,2022,and the online Registry(https://seqco.del)was created to ensure valid publication of names.The SeqCode recognizes all names validly published under the ICNP before 2022.After that date,names validly published under the SeqCode compete with ICNP names for priority.As a result,species can have only one name,either from the SeqCode or ICNP,enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes.The SeqCode is administered by the SeqCode Committee,which is comprised of the SeqCode Community and elected administrative components.Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.

Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes

Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology,new drugs and therapies,and environmental remediation.However,most uncultured microbial species along with their metabolic capacities in extreme environments,remain obscured.Here we unravel the metabolic potential of microbial dark matters(MDMs)in four deep-inland hypersaline lakes in Xinjiang,China.Utilizing metagenomic binning,we uncovered a rich diversity of 3030 metagenomeassembled genomes(MAGs)across 82 phyla,revealing a substantial portion,2363 MAGs,as previously unclassified at the genus level.These unknown MAGs displayed unique distribution patterns across different lakes,indicating a strong correlation with varied physicochemical conditions.Our analysis revealed an extensive array of 9635 biosynthesis gene clusters(BGCs),with a remarkable 9403 being novel,suggesting untapped biotechnological potential.Notably,some MAGs from potentially new phyla exhibited a high density of these BGCs.Beyond biosynthesis,our study also identified novel biodegradation pathways,including dehalogenation,anaerobic ammonium oxidation(Anammox),and degradation of polycyclic aromatic hydrocarbons(PAHs)and plastics,in previously unknown microbial clades.These findings significantly enrich our understanding of biosynthesis and biodegradation processes and open new avenues for biotechnological innovation,emphasizing the untapped potential of microbial diversity in hypersaline environments.

Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes

Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.

Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa

The oral cavity of each person is home to hundreds of bacterial species.While taxa for oral diseases have been studied using culture-based characterization as well as amplicon sequencing,metagenomic and genomic information remains scarce compared to the fecal microbiome.Here,using metagenomic shotgun data for 3346 oral metagenomic samples together with 808 published samples,we obtain 56,213 metagenome-assembled genomes(MAGs),and more than 64%of the 3589 species-level genome bins(SGBs)contain no publicly available genomes.The resulting genome collection is representative of samples around the world and contains many genomes from candidate phyla radiation(CPR)that lack monoculture.Also,it enables the discovery of new taxa such as a genus Candidatus Bgiplasma within the family Acholeplasmataceae.Large-scale metagenomic data from massive samples also allow the assembly of strains from important oral taxa such as Porphyromonas and Neisseria.The oral microbes encode genes that could potentially metabolize drugs.Apart from these findings,a strongly male-enriched Campylobacter species was identified.Oral samples would be more user-friendly collected than fecal samples and have the potential for disease diagnosis.Thus,these data lay down a genomic framework for future inquiries of the human oral microbiome.