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1. Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy

   https://doi.org/10.1128/aem.02368-24  

   Cross, Kayla; Beckman, Noelle; Jahnes, Benjamin; Sabree, Zakee L (February 2025, Applied and Environmental Microbiology)

   Rudi, Knut (Ed.)

   ABSTRACT Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorousPeriplaneta americanaover 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome “service outages” due to functional redundancy. IMPORTANCEDiet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes. 

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2. Non-invasive measurements of respiration and heart rate across wildlife species using Eulerian Video Magnification of infrared thermal imagery

   https://doi.org/10.1186/s12915-023-01555-9  

   Rzucidlo, Caroline L.; Curry, Erin; Shero, Michelle R. (March 2023, BMC Biology)

   Abstract BackgroundAn animal’s metabolic rate, or energetic expenditure, both impacts and is impacted by interactions with its environment. However, techniques for obtaining measurements of metabolic rate are invasive, logistically difficult, and costly. Red–green–blue (RGB) imaging tools have been used in humans and select domestic mammals to accurately measure heart and respiration rate, as proxies of metabolic rate. The purpose of this study was to investigate if infrared thermography (IRT) coupled with Eulerian video magnification (EVM) would extend the applicability of imaging tools towards measuring vital rates in exotic wildlife species with different physical attributes. ResultsWe collected IRT and RGB video of 52 total species (39 mammalian, 7 avian, 6 reptilian) from 36 taxonomic families at zoological institutions and used EVM to amplify subtle changes in temperature associated with blood flow for respiration and heart rate measurements. IRT-derived respiration and heart rates were compared to ‘true’ measurements determined simultaneously by expansion of the ribcage/nostrils and stethoscope readings, respectively. Sufficient temporal signals were extracted for measures of respiration rate in 36 species (85% success in mammals; 50% success in birds; 100% success in reptiles) and heart rate in 24 species (67% success in mammals; 33% success in birds; 0% success in reptiles) using IRT-EVM. Infrared-derived measurements were obtained with high accuracy (respiration rate, mean absolute error: 1.9 breaths per minute, average percent error: 4.4%; heart rate, mean absolute error: 2.6 beats per minute, average percent error: 1.3%). Thick integument and animal movement most significantly hindered successful validation. ConclusionThe combination of IRT with EVM analysis provides a non-invasive method to assess individual animal health in zoos, with great potential to monitor wildlife metabolic indices in situ. 

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3. ProTaxoVis—protein taxonomic visualisation of presence

   https://doi.org/10.1186/s12859-025-06146-9  

   Hsieh, Yin-Chen; Bockwoldt, Mathias; Heiland, Ines (December 2025, BMC Bioinformatics)

   Abstract Background:Protein presence information is an essential component of biological pathway identification. Presence of certain enzymes in an organism points towards the metabolic pathways that occur within it, whereas the absence of these enzymes indicates either the existence of alternative pathways or a lack of these pathways altogether. The same inference applies to regulatory pathways such as gene regulation and signal transduction. Protein presence information therefore forms the basis for biological pathway studies, and patterns in presence-absence across multiple organisms allow for comparative pathway analyses. Results:Here we present ProTaxoVis, a novel bioinformatic tool that extracts protein presence information from database queries and maps it to a taxonomic tree or heatmap. ProTaxoVis generates a large-scale overview of presence patterns in taxonomic clades of interest. This overview reveals protein distribution patterns, and this can be used to deduce pathway evolution or to probe other biological questions. ProTaxoVis combines and filters sequence query results to extract information on the distribution of proteins and translates this information into two types of visual outputs: taxonomic trees and heatmaps. The trees supplement their topology with scaled pie-chart representations per node of the presence of target proteins and combinations of these proteins, such that patterns in taxonomic groups can easily be identified. The heatmap visualisation shows presence and conservation of these proteins for a user-determined set of species, allowing for a more detailed view over a larger group of proteins as compared to the trees. ProTaxoVis also allows for visual quality checks of hits based on a coverage plot and a length histogram, which can be used to determine e-value and minimum protein length cutoffs. Tabular output of resulting data from the query, combined, and heatmap building step are saved and easily accessible for further analyses. Conclusions:We evaluate our tool with the phosphoribosyltransferases, a transferase enzyme family with notable distribution patterns amongst organisms of varying complexities and across Eukaryota, Bacteria, and Archaea. ProTaxoVis is open-source and available at:https://github.com/MolecularBioinformatics/ProTaxoVis. 

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4. Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

   https://doi.org/10.1186/s40168-023-01554-6  

   Ettinger, Cassandra L.; Saunders, Morgan; Selbmann, Laura; Delgado-Baquerizo, Manuel; Donati, Claudio; Albanese, Davide; Roux, Simon; Tringe, Susannah; Pennacchio, Christa; del Rio, Tijana G.; et al (May 2023, Microbiome)

   Abstract BackgroundRock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities. ResultsWe performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry. ConclusionThis catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. 

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5. Making remote sense of biodiversity: What grassland characteristics make spectral diversity a good proxy for taxonomic diversity?

   https://doi.org/10.1111/geb.13759  

   Van Cleemput, Elisa; Adler, Peter; Suding, Katharine Nash (October 2023, Global Ecology and Biogeography)

   Abstract AimThe spectral variability hypothesis (SVH) predicts that spectral diversity, defined as the variability of radiation reflected from vegetation, increases with biodiversity. While confirmation of this hypothesis would pave the path for use of remote sensing to monitor biodiversity, support in herbaceous ecosystems is mixed. Methodological aspects related to scale have been the predominant explanation for the mixed support, yet biological characteristics that vary among herbaceous systems may also affect the strength of the relationship. Therefore, we examined the influence of three biological characteristics on the relationship between spectral and taxonomic diversity: vegetation density, spatial species turnover and invasion by non‐native species. We aimed to understand when and why spectral diversity may serve as an indicator of taxonomic diversity and be useful for monitoring. LocationContinental U.S.A. Time PeriodPeak greenness in 2017. Major Taxa StudiedGrassland and herbaceous ecosystems. MethodsFor nine herbaceous sites in the National Ecological Observatory Network, we calculated taxonomic diversity from field surveys of 20 m × 20 m plots and derived spectral diversity for those same plots from airborne hyperspectral imagery with a spatial resolution of 1 m. The strength of the taxonomic diversity–spectral diversity relationship at each site was subsequently assessed against measurements of vegetation density, spatial species turnover and invasion. ResultsWe found a significant relationship between taxonomic and spectral diversity at some, but not all, sites. Spectral diversity was more strongly related to taxonomic diversity in sites with high species turnover and low invasion, but vegetation density had no effect on the relationship. Main ConclusionsUsing spectral diversity as a proxy for taxonomic diversity in grasslands is possible in some circumstances but should not just be assumed based on the SVH. It is important to understand the biological characteristics of a community prior to considering spectral diversity to monitor taxonomic diversity. 

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