Mwaikono, K. S. | bioRxiv Science

bioRxiv2025

Characterisation of Ornithobacterium hominis colonisation dynamics and interaction with the nasopharyngeal microbiome in a South African birth cohort.

Ornithobacterium hominis is a recently described Gram-negative bacterium that colonises the human nasopharynx and may be associated with poor upper respiratory tract health. Here, we describe the isolation of O. hominis from samples collected from a South African birth cohort, creating the first archive of cultured strains of the species from Africa. Sequenced genomes from this archive reveal that South African O. hominis is more similar to Australian strains than those from Southeast Asia, and that it may share genes with other members of the microbiome that are relevant for virulence, colonisation, and antibiotic resistance. Leveraging existing microbiome data from the cohort, O. hominis was found to be closely associated with bacterial co-colonisers that are rare in non-carrier individuals, including Suttonella, Helcococcus, Moraxella spp., and Gracilibacteria. Their collective acquisition has a significant impact on the diversity of nasopharyngeal communities that contain O. hominis. Individuals who have not yet acquired O. hominis have a higher abundance of Moraxella (particularly M. lincolnii) than individuals who never acquire O. hominis, suggesting that this could be a precursor state for successful colonisation. Finally, a novel co-coloniser species, Helcococcus ekapensis, was successfully isolated and sequenced. Data SummaryOrnithobacterium hominis data have been deposited under project accession ERP149886. This comprises genome sequences for isolates SA-OH-C1 (ERR13967269), SA-OH-C2 (ERR13967270), SA-OH-C3 (ERR13967271), SA-OH-C4 (ERR13967272, ERR13967275), SA-OH-C5 (ERR13967273), SA-OH-C6 (ERR13967274, ERR13967276). Previously published 16S rRNA gene data are deposited under project accessions PRJNA790843 and PRJNA548658. Helcococcus ekapensis genome data are deposited under project accession PRJEB85661. Software usedO_LIAMRFinderPlus v3.12.8: https://github.com/ncbi/amr C_LIO_LIAssembleBAC-ONT v1.1.1: https://github.com/avantonder/assembleBAC-ONT C_LIO_LIBAKTA v1.8.1: https://bakta.computational.bio/ C_LIO_LIBLAST v2.16.0: https://blast.ncbi.nlm.nih.gov/Blast.cgi C_LIO_LIComprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (RGI) tool v1.2.1: https://card.mcmaster.ca/analyze/rgi C_LIO_LIDecontam v1.12 (R package): https://github.com/benjjneb/decontam C_LIO_LIEggnog-mapper v2.0.1: http://eggnog-mapper.embl.de/ C_LIO_LIFastANI v1.1.0: https://github.com/ParBLiSS/FastANI C_LIO_LIFlye v2.9.2: https://github.com/fenderglass/Flye C_LIO_LIGuppy v6.5.7: https://community.nanoporetech.com/downloads/guppy/release_notes C_LIO_LIISEScan v1.7.2.3: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/isescan/isescan/1.7.2.3+galaxy1 C_LIO_LIMedaka v1.9.1: https://github.com/nanoporetech/medaka C_LIO_LIMEGA11: https://www.megasoftware.net/ C_LIO_LIMMseqs2 v17: https://github.com/soedinglab/MMseqs2 C_LIO_LIMothur v1.44.3: https://github.com/mothur/mothur C_LIO_LINetCoMi v1.2.0 (R package): https://github.com/stefpeschel/NetCoMi C_LIO_LIPanaroo v1.4.3: https://github.com/gtonkinhill/panaroo C_LIO_LIPHASTEST: https://phastest.ca/submissions/new C_LIO_LIProwler (commit ID c3041ba): https://github.com/ProwlerForNanopore/ProwlerTrimmer C_LIO_LIR v4.4.3: https://www.r-project.org/ C_LI Databases usedO_LIComprehensive Antibiotic Resistance Database (CARD): https://card.mcmaster.ca/ C_LIO_LIEuropean Nucleotide Archive: https://www.ebi.ac.uk/ena/ C_LIO_LIGenome Taxonomy Database (GTDB) release 09-RS220: https://gtdb.ecogenomic.org/ C_LIO_LIRefSeq release 228: https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/ C_LIO_LISILVA v132: https://www.arb-silva.de/ C_LI Impact statementFirst described in 2019, Ornithobacterium hominis is an understudied bacterium that may be associated with poor respiratory health in children. The study builds upon existing knowledge of O. hominis by describing the first African isolates of the species, its potential as a reservoir of virulence and antibiotic resistance genes in the upper respiratory tract, and the unique microbiome profile of O. hominis carriers.

microbiology↗

bioRxiv2023

A comparative study on the impact of five Desmodium species on soil microbiome reveals enrichment of selected bacterial and fungal taxa

IntroductionSeveral Desmodium spp. are used as intercrops in push-pull pest management systems to repel insect herbivores. In addition, Desmodium suppresses the parasitic weed Striga, and diversifies the soil microbiome with negative impacts on fungi. We investigated the impact of a 2-year cropping of five Desmodium species on soil microbiome populations. MethodologyTotal DNA was obtained from root zone soil samples collected from a two-years-old common garden experiment with replicated plots of five Desmodium spp. at the international centre for insect physiology and ecology (ICIPE), Mbita, Kenya. Subsequently, 16S and ITS DNA sequencing were performed and the data was analysed by using QIIME2 and Calypso. ResultsOur findings show significant differences in composition and abundance of specific microbial taxa among the Desmodium plots and the bulk soil, with a stronger shift observed for fungal community profiles than bacteria. There was, however, no significant difference in overall diversity, richness and evenness of microbial communities among the Desmodium plots and the bulk soil. Similarly, beta diversity analysis did not reveal a significant association of variation to specific Desmodium spp. plots. Discussion and conclusionThis is the first study to compare impact and association of whole soil microbiomes to different Desmodium species. Whereas long-term Desmodium cropping clearly shifts whole microbiome communities, no significant difference in overall diversity and richness of microbial populations was observed among the studied plots. However, there was a divergence of individual taxa reflected on their increased abundance in association to specific Desmodium spp., pointing towards potential impact on ecosystem services. These findings indicate that significant shifts in whole microbial populations due to Desmodium spp. and thus potentially provision of associated ecosystem services require longer cultivation periods to solidify. Future studies should focus on techniques that monitor real-time changes in microbial populations such as RNA-seq to ascertain live and dead microbes, and thus infer ecological services.

ecology↗