MeioBIOME, a modular Snakemake pipeline for the reproducible analysis of holobiont metagenomes obtained from individually sequenced microbial metazoa is developed and it is anticipated that MeioBIOME will facilitate studies of phylosymbiosis by generating high-quality host genome skims (to build well-supported host phylogenetic trees) and host-associated prokaryotic MAGs obtained from single specimens.
Abstract
Microbes closely interact with every living organism, including meiofauna (i.e., microbial eukaryotes 38 μm – 1 mm in length), and influence the development, life cycle, and evolution of diverse metazoans. Together, meiofauna and their microbiomes, collectively referred to as the holobiont, underpin biogeochemical cycles and drive decomposition of organic matter. However, our understanding of the ecological and evolutionary dynamics of meiofauna microbiomes are limited, typically owed to low-resolution 16S rRNA surveys, which cannot accurately delineate bacterial taxa. Single-specimen holobiont sequencing can help overcome the limitations of metabarcoding approaches by 1) generating metagenome-assembled genomes (MAGs) of the host microbiome and 2) recovering host single-copy genes (SCGs) to phylogenetically confirm the identity of the host organism. However, most bioinformatics pipelines for the assembly of metagenomic datasets have been developed for the assembly of high-complexity microbial communities of bulk sediment or soil samples (and cannot be used for the assembly of host genomes), rely on co-assembly approaches (which collapses strain-level genomic information of bacterial taxa), and focus on binning either prokaryotic or eukaryotic taxa. Therefore, there is a tremendous need for a computational workflow for the dual analysis of host genomes and their microbiomes. Here, we developed MeioBIOME, a modular Snakemake pipeline for the reproducible analysis of holobiont metagenomes obtained from individually sequenced microbial metazoa. We analyze publicly available single-specimen metagenomics datasets to show the utility of MeioBIOME and recover host-associated symbiont MAGs and host SCGs. Additionally, we integrate state-of-the-art binning algorithms which generate more MAGs than the DOE Joint Genome Institute metagenomic pipeline. We anticipate that MeioBIOME will facilitate studies of phylosymbiosis by generating high-quality host genome skims (to build well-supported host phylogenetic trees) and host-associated prokaryotic MAGs obtained from single specimens.
The first comparative genomic analysis of multiple isolates of a single chytrid species infecting the cyanobacterium Planktothrix agardhii is presented, suggesting that chytrids consistently express high levels of cytoskeletal genes, alongside numerous hypothetical proteins, and that zoospores may upregulate carbohydrate-binding proteins implicated in host recognition.
Katelyn M. McKindles, Kensuke Seto, Steven R. Ahrendt et al.· Aquatic Ecology· 0 citations
Microbial symbioses drive the evolutionary and functional diversification of eukaryotic clades, from single-celled protists to large invertebrates. However, our knowledge of host-associated assemblages (the “holobiont”) is limited in microscopic animal phyla with a body size <1mm, due to practical challenges such as low biomass and difficult taxonomy of host species. Marine nematodes represent an ideal case study for rapidly advancing our knowledge of bacterial-animal symbioses, representing a globally abundant invertebrate group with strong links to terrestrial and model organism species within the same phylum. Here, we sequenced the holobionts of 220 marine nematodes and generated 815 metagenome-assembled genomes (MAGs) of host-associated bacteria/archaea. Our data indicates that 20-34% of marine nematodes harbor an obligate intracellular symbiont, often with multiple endosymbionts co-occurring within the same host. Three bacterial phyla (Pseudomonadota Bacteroidota, and Verrucomicrobiota) account for three-quarters of all nematode-associated MAGs, and the majority of these holobiont MAGs represent deeply divergent lineages in the prokaryotic tree of life. The Flavobacteriaceae (a core microbiome taxon in C. elegans and other terrestrial nematodes), were consistently recovered across phylogenetically diverse marine nematode lineages, suggesting evolutionary conservation of holobiont taxa across marine and terrestrial environments. We also report a novel chemoautotroph family (Ca. Thionematobacter) recovered from nematode hosts in both deep-sea and shallow-water habitats, and report the first confirmed instance of Cardinium endosymbionts from marine invertebrates. Finally, ∼65% of nematode-associated MAGs are able to degrade chitin, via hexosaminidase, implying that benthic invertebrate holobionts make significant contributions to global carbon cycling. These results underline the importance of evaluating symbiosis in microscopic marine invertebrates, and accelerating our understanding of animal evolution and ecosystem dynamics in vast benthic habitats.
Alejandro De Santiago, M. Han, Sarah B. Hargadon et al.· bioRxiv· 0 citations
Once thought to be sterile, animal venom systems instead harbour diverse microbiomes. In some venomous lineages, bacteria contribute to venom production, while in other lineages bacteria have donated venom toxin genes via horizontal gene transfer. We studied the centipede
Lithobius forficatus
to shed new light on these topics.
L. forficatus
has an anterior venom-producing system comprising forcipules and associated venom glands, as well as a serially homologous secretory defence system comprising its posterior legs and associated telopodal glands. We used full-length 16S rRNA sequencing to characterise the bacterial microbiomes of these weaponised appendages, and of gonads and habitat soil. We found that all centipede organs harboured diverse microbiomes that overlapped substantially with soil microbiomes, with no differences between the microbiomes of male and female centipedes. While alpha diversity analysis identified significant differences in observed diversity between sample types, beta diversity analysis only identified a significant difference in microbiomes of different geographic locations. The gonads (only internal organ sample) contained the smallest number of unique bacterial operational taxonomic units and lacked a core microbiome. Finally, there was no evidence to suggest that the bacterial microbiomes directly contribute toxins to the weaponised secretions of
L. forficatus
.
Harriet Jameson, Eivind A. B. Undheim, Steve Bagby et al.· Scientific Reports· 0 citations
Myxococcota are globally distributed bacteria renowned for their remarkable ecological and biotechnological significance due to their complex lifestyles, social behaviour, and secondary metabolite production. Despite their ubiquity in diverse environments, including soil, marine, and extreme habitats, their diversity and ecological roles remain underexplored. Here, we utilized the Microflora Danica dataset, encompassing >10,000 metagenomes and >400 rRNA gene datasets from various environments in Denmark, to investigate the distribution, diversity, and metabolic potential of Myxococcota. We show that Myxococcota are ubiquitous but strongly structured by environment, with soil-associated lineages enriched in predatory and multicellular development traits, whereas aquatic-associated taxa exhibit alternative lifestyles, including anaerobic metabolism and phototrophy. Comparative genomic analysis reveals widespread potential for secondary metabolite production, hydrocarbon degradation, and organohalide transformation, alongside diverse contribution to carbon and nutrient cycling. Together, these findings redefine Myxococcota as a functionally diverse and ecologically differentiated phylum, extending beyond canonical predation and multicellularity, and underscore their promise as large reservoir of unexplored functional potential for biotechnological applications in drug discovery and environmental remediation.
F. Petriglieri, Yu Yang, Z. Kondrotaite et al.· bioRxiv· 0 citations
Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pelagibacter and Prochlorococcus, are conspicuously underrepresented. Here, we present the Great Barrier Reef Microbial Genomes Database (GBR-MGD) comprising 5,283 prokaryotic genomes obtained from GBR seawater samples using Nanopore sequencing, including a collection of high quality genomes of underrepresented groups. We show that standard short read assemblies miss these populations due to a combination of strain heterogeneity and low GC% sequencing bias. The GBR-MGD also comprises 20 chromosome-level picoeukaryote and 808,585 viral genomes, including a newly described clade of marine Crassvirales. We demonstrate the use of the GBR-MGD to identify indicator taxa that can reliably predict the effects of reef management practices, such as the establishment of marine protected zones.
Steven J. Robbins, Marko Terzin, K. Dougan et al.· bioRxiv· 2 citations
Applications across healthcare, environmental science, agriculture, biotechnology, and industry are reviewed with particular emphasis on clinical metagenomic next-generation sequencing (mNGS) for infectious disease diagnostics, antimicrobial resistance (AMR) surveillance, gut microbiome research, and precision medicine.
Ahmed Alsharksi· Razi Medical Journal· 0 citations
