Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome

Nweze, Julius Eyiuche; Schweichhart, Johannes Sergej; Angel, Roey

doi:10.1111/1462-2920.16586

Cited by 2 publications

(1 citation statement)

References 93 publications

(120 reference statements)

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“…We shared 1,182 of these RdRp HMM profiles as NeoRdRp 1.1, along with the associated RdRp domain sequences and RdRp domain sequences, and the bioinformatics pipeline at NeoRdRp (3): https:// github.com/shoichisakaguchi/NeoRdRp. NeoRdRp was used in various RNA virus identification studies (4)(5)(6).…”

Section: Introductionmentioning

confidence: 99%

NeoRdRp2 with improved seed data, annotations, and scoring

Sakaguchi,

Nakano,

Nakagawa

2024

Front. Virol.

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RNA-dependent RNA polymerase (RdRp) is a marker gene for RNA viruses; thus, it is widely used to identify RNA viruses from metatranscriptome data. However, because of the high diversity of RdRp domains, it remains difficult to identify RNA viruses using RdRp sequences. To overcome this problem, we created a NeoRdRp database containing 1,182 hidden Markov model (HMM) profiles utilizing 12,502 RdRp domain sequences. Since the development of this database, more RNA viruses have been discovered, mainly through metatranscriptome sequencing analyses. To identify RNA viruses comprehensively and specifically, we updated the NeoRdRp by incorporating recently reported RNA viruses. To this end, 557,197 RdRp-containing sequences were used as seed RdRp datasets. These sequences were processed through deduplication, clustering, alignment, and splitting, thereby generating 19,394 HMM profiles. We validated the updated NeoRdRp database, using the UniProtKB dataset and found that the recall and specificity rates were improved to 99.4% and 81.6%, from 97.2% and 76.8% in the previous version, respectively. Comparisons of eight different RdRp search tools showed that NeoRdRp2 exhibited balanced RdRp and nonspecific detection power. Expansion of the annotated RdRp datasets is expected to further accelerate the discovery of novel RNA viruses from various transcriptome datasets. The HMM profiles of NeoRdRp2 and their annotations are available at https://github.com/shoichisakaguchi/NeoRdRp.

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Section: Introductionmentioning

confidence: 99%

NeoRdRp2 with improved seed data, annotations, and scoring

Sakaguchi,

Nakano,

Nakagawa

2024

Front. Virol.

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Cellulose fermentation by the gut microbiota is likely not essential for the nutrition of millipedes

Nweze,

Gupta,

Salcher

et al. 2024

Preprint

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Millipedes are thought to depend on their gut microbiome for processing plant-litter-cellulose through fermentation, similar to many other arthropods. However, this hypothesis lacks sufficient evidence. To investigate this, we disrupted the gut microbiota of juvenileEpibolus pulchripes(tropical, CH4-emitting) andGlomeris connexa(temperate, non-CH4-emitting) using chemical inhibitors and isotopic labelling. Feeding the millipedes sterile or antibiotics-treated litter notably reduced faecal production and microbial load without major impacts on survival or weight. Bacterial diversity remained similar, withBacteroidotadominant inE. pulchripesandPseudomonadotainG. connexa. Sodium-2-bromoethanesulfonate treatment halted CH4emissions and reduced the faecalmcrAcopies inE. pulchripesafter 14 days, but emissions resumed after returning to normal feeding. Methanogens in the orderMethanobacterialesandMethanomasscilliicoccalesassociated with protists were detected using Catalysed Reporter Deposition FluorescenceIn situHybridization (CARD-FISH) on day 21, despite suppressed CH4-emission. Employing13C-labeled leaf litter and RNA-SIP revealed a slow and gradual prokaryote labelling, indicating a significant density shift only by day 21. In addition to labelling of taxa from orders well-recognized for their role in (ligno)cellulose fermentation (e.g.,Bacteroidales,Burkholderiales, andEnterobacterales), others, such as members ofDesulfovibrionaleswere also labelled. Surprisingly, labelling of the fungal biomass was somewhat quicker. Our findings suggest that fermentation by the gut microbiota is likely not essential for the millipede's nutrition.

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Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome

Cited by 2 publications

References 93 publications

NeoRdRp2 with improved seed data, annotations, and scoring

NeoRdRp2 with improved seed data, annotations, and scoring

Cellulose fermentation by the gut microbiota is likely not essential for the nutrition of millipedes

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