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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. DL-TODA: A Deep Learning Tool for Omics Data Analysis

   https://doi.org/10.3390/biom13040585  

   Cres, Cecile M.; Tritt, Andrew; Bouchard, Kristofer E.; Zhang, Ying (April 2023, Biomolecules)

   Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon. 

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3. Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

   https://doi.org/10.1128/msystems.00965-22  

   Rojas, Connie A.; Holekamp, Kay E.; Viladomat Jasso, Mariette; Souza, Valeria; Eisen, Jonathan A.; Theis, Kevin R. (January 2022, mSystems)

   Hird, Sarah M. (Ed.)

   The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas ( Crocuta crocuta ) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas’ guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host’s life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis. 

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4. Grassland restoration characteristics influence phylogenetic and taxonomic structure of plant communities and suggest assembly mechanisms

   https://doi.org/10.1111/1365-2745.13250  

   Barber, Nicholas A.; Farrell, Anna K.; Blackburn, Ryan C.; Bauer, Jonathan T.; Groves, Anna M.; Brudvig, Lars A.; Jones, Holly P.; Gibson, ed., David (August 2019, Journal of Ecology)

   Abstract Phylogenetic and species‐based taxonomic descriptions of community structure may provide complementary information about the mechanisms driving community assembly across different environments. Environmental filtering may have similar effects on taxonomic and phylogenetic diversity under the assumption of niche conservatism, whereas competitive exclusion could produce contrasting patterns in these diversity metrics. In grassland restorations, these diversity patterns might then reveal potential assembly mechanisms underlying the impacts of restoration and management conditions on community structure.We compared plant community structure (alpha diversity, composition, and within‐site beta diversity) from both phylogenetic and taxonomic perspectives. Using surveys from 120 tallgrass prairie restorations in four regions of the Midwestern United States, we examined the effects of four potential drivers or environmental gradients: precipitation in the first year of restoration, seed mix richness, time since last prescribed fire, and restoration age, and included soil conditions as a covariate.First‐year precipitation influenced taxonomic community structure, but had weak effects on phylogenetic diversity and composition. Similarly, greater seed mix richness increased taxonomic diversity but did not influence phylogenetic diversity. Taxonomic, but not phylogenetic, diversity generally was lower in older restorations and those with a longer time since the last prescribed fire. These drivers consistently explained more variation in taxonomic than phylogenetic diversity and composition, perhaps in part because species turnover was largely among related species, producing weak impacts on phylogenetic community measures.An impact of precipitation on taxonomic but not phylogenetic diversity suggests that there may not be large differences in drought tolerance among clades that would cause phylogenetic patterns to arise from this environmental filter. Declining taxonomic diversity but not phylogenetic diversity is consistent with competitive exclusion as an assembly mechanism when competition is strongest between related species.Synthesis. This research shows how studying taxonomic and phylogenetic diversity of ecosystem restorations can inform plant community ecology and help natural resource managers better predict the outcomes of restoration actions and management. 

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5. Common latitudinal gradients in functional richness and functional evenness across marine and terrestrial systems.

   Schumm, M.; Edie, S.M.; Collins, K.S.; Gómez-Bahamón, V.; Supriya, K.; White, A.E.; Price, T.D.; Jablonski, D. (July 2019, Proceedings - Royal Society. Biological Sciences)

   Functional diversity is an important aspect of biodiversity, but its relationship to species diversity in time and space is poorly understood. Here we compare spatial patterns of functional and taxonomic diversity across marine and terrestrial systems to identify commonalities in their respective ecological and evolutionary drivers. We placed species-level ecological traits into comparable multi-dimensional frameworks for two model systems, marine bivalves and terrestrial birds, and used global speciesoccurrence data to examine the distribution of functional diversity with latitude and longitude. In both systems, tropical faunas show high total functional richness (FR) but low functional evenness (FE) (i.e. the tropics contain a highly skewed distribution of species among functional groups). Functional groups that persist toward the poles become more uniform in species richness, such that FR declines and FE rises with latitude in both systems. Temperate assemblages are more functionally even than tropical assemblages subsampled to temperate levels of species richness, suggesting that high species richness in the tropics reflects a high degree of ecological specialization within a few functional groups and/or factors that favour high recent speciation or reduced extinction rates in those groups. 

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