Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Alneberg, Johannes; Karlsson, Christofer M. G.; Divne, Anna-Maria; Bergin, Claudia; Homa, Félix; Lindh, Markus V.; Hugerth, Luisa W.; Ettema, Thijs J. G.; Bertilsson, Stefan; Andersson, Anders F.; Pinhassi, Jarone

doi:10.1101/219295

Cited by 5 publications

(7 citation statements)

References 83 publications

(106 reference statements)

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“…Metagenome reads from 30 samples of the original LMO dataset were mapped to the 30 MAGs (BACLs). Reads were also mapped from 30 metagenomic samples obtained in a transect cruise 36 , where 10 stations distributed along the Baltic Sea salinity gradient where sampled at three depths (Figure 1, Supplementary Table 2). To lower the risk of including reads derived from other species, we only included reads mapping with >95% identity to the MAGs.…”

Section: Resultsmentioning

confidence: 99%

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

Sjöqvist

Zambrano

Alneberg

et al. 2020

Preprint

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Background Bacterioplankton are main drivers of biogeochemical cycles and important components of aquatic food webs. However, difficulties in culturing the majority of aquatic prokaryotic species have complicated the study of their microdiversity. Here, we present POGENOM, a software that quantifies population genomic indices from metagenome data, enabling comparative analysis of genomic diversity and differentiation in multiple species in parallel. We demonstrate POGENOM on metagenome-assembled genomes from the Baltic Sea and investigate their genomic variation using metagenome data spanning a 1700 km transect and covering seasonal variation at one station. ResultsThe majority of the investigated species, representing several major bacterioplankton clades, displayed population structure correlating significantly with environmental factors such as salinity, temperature, nutrients and oxygen, both over horizontal and vertical dimensions. Population differentiation was more pronounced over spatial than temporal scales, although some species displayed population structure correlating with season. We discovered genes that have undergone adaptation to different salinity regimes, potentially responsible for the populations' existence along the salinity range. ConclusionsWe provide a new tool for high-throughput population genomics analysis based on metagenomics data. From an evolutionary point of view, our findings emphasize the importance of physiological barriers, and highlight the role of adaptive divergence as a structuring mechanism of bacterioplankton species, despite their seemingly unlimited dispersal potential. This is of central importance when learning about how species have adapted to new environmental conditions and what their adaptive potential is in the face of Global Change.

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Section: Resultsmentioning

confidence: 99%

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

Sjöqvist

Zambrano

Alneberg

et al. 2020

Preprint

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“…We obtained 55 unique MAGs and 31 of them met the standard of high-quality draft genomes (completion >90% and contamination <5%). Since both mouse and human gut microbiota were dominated by Bacteroidetes and Firmicutes (26, 27), we analyzed these two phyla at the strain level in both, and characterized the potential function of mouse strains through KEGG orthologs and carbohydrate active enzymes. Furthermore, we detected other phyla except Bacteroidetes and Firmicutes, and discovered that some of them have the closest genome with the strains in intestinal mucus layer of laboratory rodents.…”

Section: Discussionmentioning

confidence: 99%

“…Although all specieses we found are assigned to known bacterial genera, families or orders, more than 80% species were classified to novel species based on MAG during our resolving procedure, such as Acholeplasmatales MAG:AF08 and P. excrementihominis MAG:CG14. It has been reported that uncultivated prokaryotes, such as bacteria, could be obtained by single-amplified genome and MAG approaches (26) and the Genomic Standards Consortium has been completed by minimum information about a MAG, which facilitate robust genomic analyses of bacterial genome (27). However, based on this consequence, the studies on strain-level microbiota in model animals could hardly be found.…”

Section: Discussionmentioning

confidence: 99%

Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics

Zhang

et al. 2020

Preprint

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21The laboratorial mouse harbors a unique gut microbiota with potential value for human microbiota-22 associated studies. Mouse gut microbiota has been explored at the genus and species levels, but features 23 rarely been showed at the strain level. The identification of 833,051 and 658,438 nonredundant genes of 24 faeces and gut content samples from the laboratorial C57/BL mice showed over half of these genes were 25 newly found compared to the previous mouse gut microbial gene catalogue. Metagenome-assembled 26 genomes (MAGs) was used to reconstruct 46 nonredundant MAGs belonging to uncultured specieses. These 27MAGs included members across all phyla in mouse gut (i.e. Firmicutes, Bacteroidetes, Proteobacteria, 28 Deferribacteres, Verrucomicrobia, and Tenericutes) and allowed a strain-level delineating of the mouse gut 29 microbiota. Comparison of MAGs with human gut colonies revealed distinctive genomic and functional 30 characteristics of mouse's Bacteroidetes and Firmicutes strains. Genomic characteristics of rare phyla in 31 mouse gut microbiota were demonstrated by MAG approach, including strains of Mucispirillum schaedleri, 32Parasutterella excrementihominis, Helicobacter typhlonius, and Akkermansia muciniphila. 33 Importance 34 The identification of nonredundant genes suggested the existence of unknown microbes in the mouse gut 35 samples. The metagenome-assembled genomes (MAGs) instantiated the specificity of mouse gut species and 36 revealed an intestinal microbial correlation between mouse and human. The cultivation of faeces and gut 37 contents sample validated the existence of MAGs and estimate their accuracy. Full-length 16S ribosomal 38 RNA gene sequencing enabled taxonomic characterization. This study highlighted a unique ecosystem in the 39 gut of laboratorial mice that obviously differed with the human gut flora at the strain level. The outcomes 40 may be beneficial to researches based on laboratorial mouse models. 41 42 Introduction 43The gut microbiota is a dense and diverse ecosystem (1). The associations between altered gut microbial 44 composition and various pathogenesis, such as obesity (2, 3), type 2 diabetes (4), rheumatoid arthritis (5), 45 and allergy (6), has become a research hotspot. Murine models, especially mouse, are widely used in 46 biomedical study. Many studies have showed that mouse intestinal models also play a pivotal role in human 47 gut microbial research. Some phyla in mouse intestinal flora, such as Firmicutes, Bacteroidetes, 48Proteobacteria, has resemblances with that in human (7, 8). In addition, there are plenty of similarities in 49 anatomy, genetics and physiology between mouse and human (9). These features make the mouse one of the 50 most essential model animals in laboratory. However, mouse gut microbiota could be influenced by many 51 factors, including diet, ambient temperature and cleanliness. Hence, there are still some distinctions between 52 human and mouse gut microbiota. Previous studies have showed that over 50% of genera in mouse gut 53 microbi...

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“…Whole genome sequences of select Bacteroidota (and Escherichia coli K-12 as referent) downloaded from NCBI were split into 250bp sequences using FASTAsplitting software (https://www.bioinformatics.org/sms2/split_fasta.html) to approximate the range of in vivo DNA samples which are commonly used for shotgun sequencing (49). The sequences for each respective genome were then used as inputs for taxonomic classification in BV-BRC as well as for assessment of matching protein sequences using BLASTX.…”

Section: Metagenomics Of Bacteroidotamentioning

confidence: 99%

The basis of antigenic operon fragmentation inBacteroidotaand commensalism

Bank

Singh

Grubb

et al. 2023

Preprint

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The causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism within the phylum Bacteroidota remain unclear. Using the classical lipopolysaccharide/O-antigen rfb operon in Enterobacteriaceae as a surface antigen model (5-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification, we characterized the architecture/conservancy of the entire rfb operon in Bacteroidota. Analyzing complete genomes, we discovered that most Bacteroidota have the rfb operon fragmented into non-random gene-singlets and/or doublets/triplets, termed "minioperons". To reflect global operon integrity, duplication, and fragmentation principles, we propose a five-category (infra/supernumerary) cataloguing system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in specific micro-niches. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes. DNA insertions overrepresenting DNA-exchange-avid species, impact functional metagenomics by inflating gene-based pathway inference and overestimating "extra-species" abundance. Using bacteria from inflammatory gut-wall cavernous micro-tracts (CavFT) in Crohns Disease, we illustrate that bacteria with supernumerary-fragmented operons cannot produce O-antigen, and that commensal/CavFT Bacteroidota stimulate macrophages with lower potency than Enterobacteriaceae, and do not induce peritonitis in mice. The impact of "foreign-DNA" insertions on pro-inflammatory operons, metagenomics, and commensalism offers potential for novel diagnostics and therapeutics.

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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Cited by 5 publications

References 83 publications

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

Revealing ecologically coherent population structure of uncultivated bacterioplankton with POGENOM

Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics

The basis of antigenic operon fragmentation inBacteroidotaand commensalism

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