Biology subjects

Woodward, C.

Publications and source records attributed to Woodward, C..

5 recordsLinked to original sources

bioRxiv2024

Targeted protein evolution in the gut microbiome by diversity-generating retroelements

Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.

microbiology↗

bioRxiv2024

RelQ-mediated alarmone signaling regulates growth, sporulation, and stress-induced biofilm formation in Clostridioides difficile

The bacterial stringent response (SR) is a conserved transcriptional reprogramming pathway mediated by the nucleotide signaling alarmones, (pp)pGpp. The SR has been implicated in antibiotic survival in Clostridioides difficile, a biofilm- and spore-forming pathogen that causes resilient, highly recurrent C. difficile infections. The role of the SR in other processes and the effectors by which it regulates C. difficile physiology are unknown. C. difficile RelQ is a clostridial alarmone synthetase. Deletion of relQ dysregulates C. difficile growth in unstressed conditions, affects susceptibility to antibiotic and oxidative stressors, and drastically reduces biofilm formation. While wild-type C. difficile displays increased biofilm formation in the presence of sub-lethal stress, the {Delta}relQ strain cannot upregulate biofilm production in response to stress. Deletion of relQ slows spore accumulation in planktonic cultures but accelerates it in biofilms. This work establishes biofilm formation and sporulation as alarmone-mediated processes in C. difficile and reveals the importance of RelQ in stress-induced biofilm regulation.

microbiology↗

bioRxiv2021

Ancient DNA and microfossils reveal dynamics of three harmful dinoflagellate species off Eastern Tasmania, Australia, over the last 9,000 years

Harmful algal blooms (HABs) have significantly impacted the seafood industry along the Tasmanian east coast over the past four decades. To investigate the history of regional HABs, we applied sedimentary ancient DNA analyses (sedaDNA) to coastal sediments up to [~]9 000 years old collected inshore and offshore Maria Island, Tasmania. We used metagenomic shotgun sequencing combined with a hybridisation capture array ( HABbaits1) to target harmful dinoflagellates of the genera Alexandrium, Gymnodinium, and Noctiluca scintillans. Bioinformatic analyses were used to verify sedaDNA sequences and their presence in older layers, especially for microreticulate cyst forming species including Gymnodinium catenatum due to its important role in shellfish toxicity. Our results show that the Alexandrium genus (up to 854 and 20 reads per sample inshore and offshore, respectively, based on capture-data) has been present off eastern Tasmania within the last [~]8 307 years. For G. catenatum we detected a total of only 9 unambiguously verified reads sporadically between [~]7 638 years ago and the present in the offshore core. We recovered verified sedaDNA of the fragile, non-fossilising species N. scintillans, along with evidence of increased relative abundance from 2010, consistent with plankton surveys. This study identifies challenges regarding sedaDNA sequence validation of some species (in particular, for G. catenatum), and provides guidance for the development of tools to monitor past and present HAB species and events, and to improve future HAB event predictions. HighlightsO_LIMetagenomic sedaDNA and hybridisation capture enabled analyses of harmful dinoflagellates off Tasmania C_LIO_LISequence validation was used to confirm the presence of Alexandrium spp., Gymnodinium spp. and Noctiluca scintillans C_LIO_LIAlexandrium and Gymnodinium have been present in Tasmanian waters during the past [~]9 000 years C_LIO_LINoctiluca scintillans sedaDNA derived relative abundance correlates with its recorded increase since 2010 C_LI

genomics↗

bioRxiv2020

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture baits technique to target marine eukaryote sedaDNA (specifically, phytoplankton, Phytobaits1; and harmful algal bloom taxa, HABbaits1), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the new bioinformatic tool HOPS to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, the Ancient: Default (A:D) sequences ratio, here positively correlated with subseafloor depth, and generated the first-ever DNA damage profiles of a key phytoplankton, the ubiquitous coccolithophore Emiliania huxleyi. Our study opens new options for the detailed investigation of marine eukaryotes and their evolution over geological timescales.

genomics↗

bioRxiv2019

Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve

Increasing evidence supports the importance of the breast milk microbiome in seeding the infant gut. However, the origin of bacteria in milk and the process of milk microbe-mediated seeding of infant intestine need further elucidation. Presumed sources of bacteria in milk include locations of mother-infant and mother-environment interactions. We investigate the role of mother-infant interaction on breast milk microbes. Shotgun metagenomics and 16S rRNA gene sequencing identified milk microbes of mother-infant pairs in breastfed infants and in infants that have never latched. Although breast milk has low overall biomass, milk microbes play an important role in seeding the infant gut. Breast milk bacteria were largely comprised of Staphylococcus, Streptococcus, Acinetobacter, and Enterobacter primarily derived from maternal areolar skin and infant oral sites in breastfeeding pairs. This suggests that the process of breastfeeding is a potentially important mechanism for propagation of breast milk microbes through retrograde flux via infant oral and areolar skin contact. In one infant delivered via Caesarian section, a distinct strain of Bifidobacteria breve was identified in maternal rectum, breast milk and the infants stool potentially suggesting direct transmission. This may support the existence of microbial translocation of this anaerobic bacteria via the enteromammary pathway in humans, where maternal bacteria translocate across the maternal gut and are transferred to the mammary glands. Modulating sources of human milk microbiome seeding potentially imply opportunities to ultimately influence the development of the infant microbiome and health.

microbiology↗