Biology subjects

Green, S. J.

Publications and source records attributed to Green, S. J..

9 recordsLinked to original sources

bioRxiv2026

Shotgun metagenomic and untargeted metabolomic analysis of gut microbiome associated with peripheral artery disease

Background: While the human gut microbiome is a potentially important and modifiable risk factor for cardiovascular diseases, the links between the gut microbiome and peripheral artery disease (PAD) and its clinical subgroups (claudication and chronic limb-threatening ischemia; CLTI) are not well understood. Methods: We used shotgun metagenomics and untargeted metabolomics to analyze the fecal samples of people with PAD and age- and sex-matched non-PAD controls collected in a cross-sectional manner. We used functional prediction pathways, a network analysis, and weighted gene co-expression network analysis of metagenomic, metabolomics, and clinical data to better understand PAD-associated dysbiosis. Results: Alpha and beta diversity were similar between the PAD (n=78) and non-PAD (n=20) groups. Differentially abundant species were dominated by those belonging to the Lachnospiraceae, Ruminococcaceae and Enterobacteriaceae families. Fecal butyrate levels were reduced between the non-PAD and PAD groups, but differences were not statistically significant. There was significantly reduced alpha diversity in the samples of the CLTI compared to claudication subgroup. Abundance of multiple butyrate producers were greater in the claudication group compared to CLTI. Network analysis revealed 5 meta-modules, each with specific associations to PAD presentation and metabolomic profiles, and species that are both top module hubs and differentially abundant between groups. Community interconnectedness appears to increase in claudication, followed by community disintegration in CLTI. Conclusions: This metagenomic-metabolomic analysis of the gut microbiome of individuals with PAD, highlights the importance of studying functional capacity, diversity, and connectivity between species. Microbial modules may allow an integrative view of the microbial ecology relevant to presence and progression of PAD.

microbiology↗

bioRxiv2026

Using carrier DNA in ultra-low input library preparations for next-generation sequencing

The purpose of this study was to evaluate the use of carrier DNA (i.e., exogenous DNA spike-in) for shotgun metagenome sequencing of ultra-low levels (less than 50 picograms) of metagenomic DNA. We hypothesized that carrier DNA would improve the robustness of library preparation for samples with DNA concentrations below detection by providing a tangible amount of known DNA thereby bringing total DNA concentrations closer to recommended input ranges for metagenomic library kits. We employed adaptive PCR cycling using an iconPCR instrument (N6tec) to allow dynamic thermocycling until sufficient library for sequencing was amplified, regardless of input DNA concentration. Libraries were sequenced and mapped to reference genomes of lambda and mock community organisms, and outcome measures included total reads, on-target reads, evenness of coverage across 10 organisms within each mock community, and PCR duplication rate. We demonstrate that libraries can be prepared down to 50 femtograms of input DNA, but that there is a strong correlation between input DNA concentration and PCR duplication rate. The utility of spiking in carrier DNA is equivocal as it mildly negatively impacts the observed distribution of mock communities and serves as a loss of sequencing output. Although the loss of sequencing capacity due to carrier DNA can be partially offset by reduced loss of data from PCR duplication, carrier DNA spike-in is not recommended for routine library preparation of ultra-low input samples. Adaptive cycling allows for appropriate cycling conditions when input DNA concentrations are below detection.

microbiology↗

bioRxiv2024

Evidence of Silencing of Intestinal Inflammatory and Immune Transcripts Following Induction of Joint Inflammation

Disrupted intestinal epithelial barrier function has been proposed to be integral to rheumatoid arthritis (RA) progression and pathogenesis. To further define the molecular pathways in synovial inflammation and the response of the intestinal tissues, we have used a rat model of mono-joint inflammatory arthritis, induced by intra-articular injection of Complete Freunds adjuvant (CFA). The predominant inflammatory response of a single injection of the adjuvant into the knee joint resulted in rapid and reproducible formation of a fibrotic myeloid-infiltrated synovial pannus. Our aim was to determine how intestinal tissues, including the proximal and distal ileum and distal colon, responded to inflammatory changes in the synovium in a temporally coordinated manner by comparing their transcriptomic landscapes using RNASeq analyses. We confirmed the timeline of joint inflammation by knee joint swelling measurement, increased synovial fluid levels of bikunin (a component of both the acute phase protein pre-alpha-inhibitor and inter-alpha-inhibitor) and demonstrated a self-correcting response of trabecular and cortical bone to the CFA challenge. Intestine-specific responses were monitored by 16S microbiome amplicon sequencing, histopathology for mucus layer integrity, and immune cell immunohistochemistry. We present data that shows the intestinal tissue displays an allostatic response to the acute joint inflammation and was region specific. The ileum primarily responded with increased mucus secretion and silencing of T-cell specific pathways, whereas the colon showed a transient upregulation of macrophages, with a broader suppression of immune related and metabolic pathway related transcripts. Interestingly, many neuropathways were activated early but then suppressed later in both the ileum and colon. There were only insignificant changes in the fecal microbiome composition in ileum or colon post-CFA administration. In summary, our data show for the first time a suppression of intestinal inflammatory and immune responses following the induction of joint inflammation and only minimal and transient changes in the microbiome. The results help clarify the molecular responses of intestinal tissues to inflammatory stresses that accompany the pathogenesis of inflammatory joint diseases.

cell biology↗

bioRxiv2023

Short- and long-term effects of continuous compost amendment on soil microbiome community

Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Yaar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 L/m2). Microbial community dynamics in the soils was examined by high-and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9-10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost-dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization. HighlightsO_LIDose-dependent changes in soil microbiome structure by manure compost application C_LIO_LIDynamic short-and long-term changes in soil microbiomes by compost amendment C_LIO_LIClimate, soil properties and management influence compost-amendment effects C_LIO_LIImmediate and temporal cumulative effects of compost on soil and {beta} diversity C_LI

microbiology↗

bioRxiv2020

Genetic Evidence for Selective Transfer of Microbes Between the International Space Station and an Astronaut

Microbial transfer from the environment can influence a persons health, but relevant studies often have confounding variables and short durations. Here, we used the unique environment of the International Space Station (ISS) to track movement of microbes between an astronauts commensal microbiomes and their environment. We identified several microbial taxa, including Serratia proteamaculans and Rickettsia australis which appear to have been transferred from the ISS to the commensal microbiomes of the astronaut. Strains were matched at the SNP and haplotype-level, and notably some strains persisted even after the astronauts return to Earth. Some transferred taxa correspond to secondary strains in the ISS environment, suggesting that transfer may be mediated by evolutionary selection. Finally, we show evidence that the T-Cell repertoire of the astronaut changes to become more specific to environmental taxa, suggesting that continual microbial and immune monitoring can help guide spaceflight mission planning, health monitoring, and habitat design.

microbiology↗

bioRxiv2019

Chimpanzees use advanced spatial cognition to plan least-cost routes

While the ability of naturally ranging animals to recall the location of food resources and use straight-line routes between them has been demonstrated in several studies, it is not known whether animals can use knowledge of their physical landscape to plan least-cost routes. This ability is likely to be particularly important for animals living in highly variable energy landscapes, where movement costs are exacerbated. Here, we used least-cost modelling to investigate whether chimpanzees (Pan troglodytes) living in a rugged, montane environment use advanced cognitive skills to plan energy efficient routes. We used a subset of chimpanzee movement segments together with the available laboratory measurements of chimpanzee energy expenditure to assign movement costs which were incorporated in an anisotropic least-cost model and straight-line null model. The least-cost model performed better than the straight-line model across all parameters, and linear mixed modelling showed a strong relationship between the cost of observed chimpanzee travel and predicted least-cost routes. To our knowledge, our study provides the first example of spatial memory for landscape and the ability to plan least-cost routes in non-human animals. These cognitive abilities may be a key trait that have enabled chimpanzees to maintain their energy balance in a low-resource environment. Our findings provide a further example of how the advanced cognitive complexity of hominids have facilitated their adaptation to a variety of environmental conditions and lead us to hypothesise that landscape complexity may play a role in shaping cognition.

animal behavior and cognition↗

bioRxiv2019

From ridge tops to ravines: landscape drivers of chimpanzee ranging patterns

Recent improvements in tracking technologies have resulted in a growing number of fine-scale animal movement studies in a variety of fields from wildlife management to animal cognition. Most studies assume that an animals \"optimal\" foraging route is linear, ignoring the role the energy landscape can play in influencing movement efficiency. Our objective was to investigate whether landscape features that affect movement costs; topographic variation, and super and substrate, influence the movement of chimpanzees (Pan troglodytes) in a rugged, montane environment. We tested for route re-use and preferential use of human-made trails and ridge tops using 14 months of focal follow data from 14 individuals and maps of established chimpanzee trails. Chimpanzees travelled on human-made trails significantly more than expected and showed weak preference for use of ridge tops for travel. Line density analysis demonstrated route re-use in chimpanzees and uncovered a network of high-use routes across their range. To our knowledge, this is the first study to empirically demonstrate route re-use and preferential use of human-made trails for travel by chimpanzees. We discuss the energetic and cognitive benefits of trail use and the implications for chimpanzee sociality. By applying the latest GIS analytical techniques to fine-scale movement data, this study demonstrates the importance of incorporating landscape features in predictive animal movement models.

animal behavior and cognition↗

bioRxiv2019

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants. Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt. We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms.\n\nSignificance StatementThis study examines the potential for microbial communities to provide insight into stresses experienced by their eukaryotic host organisms, through profiling of metagenomes and metatranscriptomes. Our study uses plant host-associated microorganisms as an in vivo and in situ microsensor to identify environmental stresses experienced by the microbial community and by the plant. Transcriptionally active host-associated microbial communities are responsive in a highly specific manner to environmental conditions. Conversely, host transcriptome sequencing provides only a very general stress response. This study is a proof-of-concept for the use of microbial communities as microsensors, with a great potential for interrogation of a wide range of host systems.

microbiology↗

bioRxiv2018

Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP

Emiliania huxleyi is a bloom forming microalga that impacts the global sulfur cycle by producing large amounts of dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide (DMS). Top-down regulation of E. huxleyi blooms is attributed to viruses and grazers, however, the possible involvement of algicidal bacteria in bloom demise is still elusive. We isolated from a North Atlantic E. huxleyi bloom a Roseobacter strain, Sulfitobacter D7, which exhibited algicidal effects against E. huxleyi upon co-culturing. Both the alga and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore establishing this host-pathogen system as an attractive, ecologically relevant model for studying alga-bacterium interaction in the oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce high amounts of methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific response, in which E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter D7 infection. Intriguingly, exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in a resistant algal strain to the bacterial pathogen. This DMSP-dependent pathogenicity was highly specific as compared to supplementation of propionate and glycerol. We propose a novel function for DMSP, in addition to its central role in mutualistic interactions, as a mediator of bacterial virulence that may regulate E. huxleyi blooms.

microbiology↗