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1. Critical assessment of pan-genomic analysis of metagenome-assembled genomes

   https://doi.org/10.1093/bib/bbac413  

   Li, Tang; Yin, Yanbin (September 2022, Briefings in Bioinformatics)

   Abstract Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi’o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi’o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies. 

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2. Draft Metagenome-Assembled Genome Sequence of a Novel Citricoccus Species from Agricultural Soil in Western Colorado

   https://doi.org/10.1128/mra.00359-22  

   O’Toole, Paul; Daly, Rebecca A; Keshavarz_Afshar, Reza; Shaffer, Michael; Wrighton, Kelly C; McGivern, Bridget B (January 2023, Microbiology Resource Announcements)

   Gill, Steven R (Ed.)

   Members of the genusCitricoccusare recognized as salt-tolerant soil microorganisms. Here, we report the metagenome-assembled genome sequence of a novelCitricoccusspecies recovered from untilled, surface agricultural soils in western Colorado. 

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3. A Mollicutes Metagenome-Assembled Genome from the Gut of the Pteropod Limacina rangii

   https://doi.org/10.1128/mra.00752-22  

   Pimentel, Zachary T.; Thibodeau, Patricia S.; Song, Bongkeun; Zhang, Ying (December 2022, Microbiology Resource Announcements)

   Stewart, Frank J. (Ed.)

   ABSTRACT A nearly complete genome of an uncultured Mollicutes sp. was obtained from the metagenome of the gut of Limacina rangii (open-ocean snail), an important grazer and prey for higher trophic animals along the rapidly warming region of the western Antarctic Peninsula. 

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4. Metagenome-assembled genome sequences of two cyanobacterial cultures from Homa Bay County, Kenya

   https://doi.org/10.1128/mra.01205-23  

   Brown, Katelyn M; Ward, Christopher S; Bullerjahn, George S (March 2024, Microbiology Resource Announcements)

   Thrash, J Cameron (Ed.)

   Metagenome-assembled genomes were generated for two xenic cyanobacterial strains collected from aquatic sources in Kenya and sequenced by NovaSeq S4. Here, we report the classification and genome statistics of Microcystis panniformis WG22 and Limnospira fusiformis. 

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5. Genome sequence of Nitrosopumilus adriaticus CCS1 assembled from an ammonia-oxidizing enrichment culture

   https://doi.org/10.1128/mra.00692-24  

   Li, Muzi; Thieringer, Patrick H; Bayer, Barbara; Kellom, Matthew; Santoro, Alyson E (December 2024, Microbiology Resource Announcements)

   Stedman, Kenneth M (Ed.)

   ABSTRACT We report the metagenome-assembled genome of an ammonia-oxidizing archaeon that is closely related toNitrosopumilus adriaticusNF5 but shows distinct genomic features compared to strain NF5. 

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