Biology subjects

Orr, R. J. S.

Publications and source records attributed to Orr, R. J. S..

8 recordsLinked to original sources

bioRxiv2025

Longitudinal analysis of the hand microbiome in response to chlorine-based antiseptic use during a military field exercise

Hand hygiene is essential for infection control, yet the impact of frequent antiseptic use on the skin microbiome, which is crucial for skin barrier function and pathogen exclusion, remains underexplored, especially in field conditions. In high-risk military settings, there is a need for safe, multipurpose antiseptics that avoid the drawbacks of alcohol-based options, including skin irritation, flammability, and unsuitability for wound application. We conducted a longitudinal study during the Norwegian-led military exercise Cold Response 2022 to assess the effects of repeated use of stabilized hypochlorous acid, a non-alcoholic antiseptic, on the hand microbiome of soldiers in a field environment. Participants used either the chlorine-based antiseptic (n = 20) or standard hygiene practices, mainly alcohol-based sanitizers (n = 19), for 10 days. Skin swabs from hands and untreated forearms were collected at baseline, post-intervention, and three weeks after discontinuation, and analyzed using 16S rRNA sequencing. Overall, our data revealed that field exposure accounted for more variation in bacterial composition than antiseptic use. When comparing alpha and beta diversity trajectories between the two antiseptic groups, there was minimal divergence during active field use, but a significant post-treatment increase in alpha diversity associated with the use of chlorine-based antiseptic. In contrast, untreated forearms showed no such group-level differences. These findings suggest that antiseptic-driven microbiome shifts are most apparent during recovery, with non-alcoholic formulations supporting faster recolonization after treatment. Stabilized hypochlorous acid represents a promising alternative to standard alcohol-based antiseptics for military personnel. IMPORTANCEEffective hand hygiene reduces pathogen transmission, but its influence on the skin microbiome has rarely been studied. Our research emphasizes the importance of longitudinal assessments by identifying greater antiseptic-driven differences occurring after cessation of treatment than during repeated use. Service members frequently use antiseptics in challenging environments, highlighting the operational need for a non-alcoholic, multipurpose product that can be safely used on both intact skin and wounds. Our findings suggest that a chlorine-based non-alcoholic antiseptic permits faster recovery of bacterial diversity after perturbation, informing product selection and hygiene policies in defense and other high-risk settings.

microbiology↗

bioRxiv2024

Skin bacterial community dynamics of hands and forearms before and after military field exercise

The human skin microbiome is crucial for skin health and immunity, especially in the context of extreme conditions faced by military personnel. Soldiers encounter unique stressors and hygienic challenges that can impact the microbial composition of their skin during field exercises and in regular occupational settings. In this study, we aimed to investigate the impact of a military field exercise on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study during the NATO exercise Cold Response 2022, involving Norwegian soldiers (n = 19) engaged in outdoor training operations. Skin swabs were taken from soldiers hands and forearms directly before and after the 10-day winter field exercise, and following a 3-week post-exercise leave. Our results reveal hand and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers microbiomes became more similar during the exercise, followed by divergence in the leave period. Neither skin site returned to original composition at follow-up, indicating that field exercises may have lasting effects on the microbiome. Our findings highlight the impact of outdoor exposure on microbial communities and suggest that resilience and stability differ between skin sites. ImportanceOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the bodys first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome, but can also inform hygiene management and disease prevention in comparable situations.

microbiology↗

bioRxiv2024

A robustly rooted tree of eukaryotes reveals their excavate ancestry.

The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start-point for the evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling, and limited phylogenetic signal. Here, we estimate the root of the eToL with unprecedented resolution based on a new, much larger, dataset of mitochondrial proteins which includes all known eukaryotic supergroups. Our comprehensive analyses with state-of-the-art phylogenetic models reveal that the eukaryotic root lies between two multi-supergroup assemblages: Opimoda+ and Diphoda+. Compellingly, this position is consistently supported across different models and robustness analyses. Notably, groups containing typical excavates are placed on both sides of the root, suggesting the complex features of the excavate cell architecture trace back to LECA. This study is the most comprehensive phylogenetic investigation of the eukaryote root to date, shedding light on the ancestral cells from which extant eukaryotes arose and providing a crucial framework for investigating the origin and evolution of canonical eukaryotic features.

evolutionary biology↗

bioRxiv2023

Extreme mitochondrial reduction in a novel group of free-living metamonads.

Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered mitochondrion-related organelles (MROs) with reduced functions relative to aerobic mitochondria, however the degree of reduction varies markedly over the metamonad tree. To further investigate metamonad MRO diversity, we generated high quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we informally named the BaSk (Barthelonids+Skoliomonads) clade, which emerges as a deeply branching sister group to the Fornicata, a metamonad phylum that includes parasitic and free-living flagellates. Extensive bioinformatic analyses of the manually curated gene models showed that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster (ISC) assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system (SMS) Fe/S cluster pathway through lateral gene transfer (LGT). One of the isolates, Skoliomonas litria, appears to have undergone further mitochondrial reduction having lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade is unprecedented and demonstrates that mitochondrial functions, under some conditions, may be completely lost even in free-living organisms.

genomics↗

bioRxiv2020

A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution

Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we alleviate this issue by presenting the molecular sequences of 165 cheilostome bryozoan species from New Zealand waters. New Zealand is our geographic region of choice as its cheilostome fauna is taxonomically, functionally and ecologically diverse, and better characterized than many other such faunas in the world. Using this most taxonomically broadly-sampled and statistically-supported cheilostome phylogeny comprising 214 species, when including previously published sequences, we tested several existing systematic hypotheses based solely on morphological observations. We find that lower taxonomic level hypotheses (species and genera) are robust while our inferred trees did not reflect current higher-level systematics (family and above), illustrating a general need for the rethinking of current hypotheses. To illustrate the utility of our new phylogeny, we reconstruct the evolutionary history of frontal shields (i.e., a calcified bodywall layer in ascus-bearing cheilostomes) and asked if its presence has any bearing on the diversification rates of cheilostomes.

evolutionary biology↗

bioRxiv2020

Compartmentalization of mRNAs in the giant, unicellular green algae Acetabularia acetabulum

Acetabularia acetabulum is a single-celled green alga previously used as a model species for studying the role of the nucleus in cell development and morphogenesis. The highly elongated cell, which stretches several centimeters, harbors a single nucleus located in the basal end. Although A. acetabulum historically has been an important model in cell biology, almost nothing is known about its gene content, or how gene products are distributed in the cell. To study the composition and distribution of mRNAs in A. acetabulum, we have used quantitative RNA-seq to sequence the mRNA content of four sections of adult A. acetabulum cells. We found that although mRNAs are present throughout the cell, there are large pools of distinct mRNAs localized to the different subcellular sections. Conversely, we also find that gene transcripts related to intracellular transport are evenly distributed throughout the cell. This distribution hints at post-transcriptional regulation and selective transport of mRNAs as mechanisms to achieve mRNA localization in A. acetabulum.

cell biology↗

bioRxiv2020

Molecular phylogeny of historical micro-invertebrate specimens using de novo sequence assembly

Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we present a pipeline that utilizes both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among understudied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer sequencing of air-dried bryozoans, utilizing a recent library preparation method for low DNA input. We use the de novo mitogenome assembly from the target specimen itself as reference for iterative mapping, and the comparison thereof. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree. Finally, the methodological success is emphasized by circularizing a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships between species.

evolutionary biology↗

bioRxiv2018

The genome of the plague-resistant great gerbil reveals species-specific duplication of an MHCII gene

The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious diseases and is defined as a key reservoir species for plague (Yersinia pestis). Studies from the wild have shown that the great gerbil is largely resistant to plague but the genetic basis for resistance is yet to be determined. Here, we present a highly contiguous annotated genome assembly of great gerbil, covering over 96 % of the estimated 2.47 Gb genome. Comparative genomic analyses focusing on the immune gene repertoire, reveal shared gene losses within TLR gene families (i.e. TLR8, TLR10 and all members of TLR11-subfamily) for the Gerbillinae lineage, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes. The great gerbil genome provides new insights into the genomic landscape that confers immunological resistance towards plague. The high affinity for Yersinia epitopes could be key in our understanding of the high resistance in great gerbils, putatively conferring a faster initiation of the adaptive immune response leading to survival of the infection. Our study demonstrates the power of studying zoonosis in natural hosts through the generation of a genome resource for further comparative and experimental work on plague survival and evolution of host-pathogen interactions.

genomics↗