Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities

Background:Synthetic microbial communities,with different strains brought together by balancing their nutrition and promoting their interactions,demonstrate great advantages for exploring complex performance of communities and for further biotechnology applications.The potential of such microbial communities has not been explored,due to our limited knowledge of the extremely complex microbial interactions that are involved in designing and controlling effective and stable communities.Results:Genome-scale metabolic models(GEM)have been demonstrated as an effective tool for predicting and guiding the investigation and design of microbial communities,since they can explicitly and efficiently predict the phenotype of organisms from their genotypic data and can be used to explore the molecular mechanisms of microbehabitats and microbe-microbe interactions.In this work,we reviewed two main categories of GEM-based approaches and three uses related to design of synthetic microbial communities:predicting multi-species interactions,exploring environmental impacts on microbial phenotypes,and optimizing community-level performance.Conclusions:Although at the infancy stage,GEM-based approaches exhibit an increasing scope of applications in designing synthetic microbial communities.Compared to other methods,especially the use of laboratory cultures,GEM-based approaches can greatly decrease the trial-and-error cost of various procedures for designing synthetic communities and improving their functionality,such as identifying community members,determining media composition,evaluating microbial interaction potential or selecting the best community configuration.Future efforts should be made to overcome the limitations of the approaches,ranging from quality control of GEM reconstructions to community-level modeling algorithms,so that more applications of GEMs in studying phenotypes of microbial communities can be expected.

Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem

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.

Genomic insights into versatile lifestyle of three new bacterial candidate phyla

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.

The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis

The division of organisms on the Tree of Life into either a three-domain(3D)tree or a two-domain(2D)tree has been disputed for a long time.Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker,there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms.Here,we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life.Meanwhile,we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes.Furthermore,we propose three major directions for future research on exploring the“next one”closest Eukaryote relative,deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects,and understanding the roles of horizontal gene transfer,viruses,and mobile elements in eukaryogenesis.

The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea

Impact statement The applications of marker gene concatenation have been advanced to resolve the key questions in the Tree of Life.However,the interphylum evolutionary relationship between Korarchaeota of TACK(Thaumarchaeota,Aigarchaeota,Crenarchaeota,Korarchaeota)and Asgard archaea remains uncertain.We applied a marker gene ranking procedure to examine their evolutionary history.Our updated trees showed confident placements of(1)Korarchaeota as the basal branch to other TACK archaea and as a sister group to Asgard archaea;(2)Njordarchaeota at basal branch to Korarchaeota instead of within Asgard archaea.They highlight the importance of evaluating marker genes for phylogeny inference of the Archaea domain.