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Abstract Anaerobic gut fungi (AGF,Neocallimastigomycota) represent a phylum of zoospore-producing fungi inhabiting the gastrointestinal tracts of herbivores. Twenty mammalian-affiliated genera (M-AGF) and two tortoise-affiliated genera (T-AGF) have been described so far. Here, we report on three additional novel T-AGF isolates obtained from Texas and sulcata tortoises. Phylogenetic analysis using the D1-D2 regions of the large ribosomal RNA subunit (D1-D2 LSU), RNA polymerase II large subunit (RPB1), internal transcribed spacer-1 region (ITS1), and transcriptomics-enabled phylogenomic analysis clustered these strains into three distinct, deep-branching clades, closely related to previously described T-AGF genusTestudinimyces. All isolates displayed filamentous rhizoidal growth patterns and produced monoflagellated zoospores. Unique morphological characteristics included the production of elongated, thick, nucleated structures in GX isolates, the formation of thin hair-like projections on sporangial walls in SR isolates, and irregularly shaped sporangia in TM isolates. All strains grew optimally at 32-35 °C and showed distinct substrate utilization capacity (e.g., growth on pectin, chitin, galactose). LSU analyses revealed GX isolates as the first cultured representatives of tortoise-affiliated but previously uncultured lineage NY56, while SR and TM strains have not been encountered in prior culture-independent AGF surveys. We propose to accommodate these isolates in three new genera and species –Gopheromyces tardescens(GXA2),Gigasporangiomyces pilosus(SR0.6), andKelyphomyces adhaerens(TM0.3). Further, based on the ecological, physiological, and phylogenetic distinctions between T-AGF and M-AGF, we propose to establish a new family (Testudinimycetaceae) to accommodate the generaTestudinimyces, Gopheromyces,Gigasporangiomyces,andKelyphomyces, within a new order (Testudinimycetales), and amend the description ofNeocallimastigalesto circumscribe M-AGF genera only. 

Members of the phylumAcidobacteriotainhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of variousAcidobacteriotalineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. ClassesTerriglobia,Vicinamibacteria,BlastocatelliaandThermoanaerobaculiawere highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classesAminicenantiaandHolophagaeshowed preferences to non-soil habitats. However, while specific preferences were observed, mostAcidobacteriotalineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of theAcidobacteriota. The observed lack of strong habitat specialization and habitat-transition-driven lineage evolution in theAcidobacteriotasuggest ready cross-colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment ofAcidobacteriotaas a major component in soil microbiomes post-ecosystem disturbance events or during pedogenesis. 

Abstract Radiation enteritis is a frequently encountered issue for patients receiving radiotherapy and has a significant impact on cancer patients' quality of life. The gut microbiota plays a pivotal role in intestinal function, yet the impact of irradiation on gut microorganisms is not fully understood. This study explores the gastroprotective effect and gut microbiome-modulating potential of ubiquinol (Ubq), the reduced form of the powerful antioxidant CoQ-10. For this purpose, male albino rats were randomly assigned to four groups: Control, IRR (acute 7 Gy γ-radiation), Ubq_Post (Ubq for 7 days post-irradiation), and Ubq_Pre/Post (Ubq for 7 days pre and 7 days post-irradiation). The fecal microbiomes of all groups were profiled by 16S rRNA amplicon sequencing followed by bioinformatics and statistical analysis. Histopathological examination of intestinal tissue indicated severe damage in the irradiated group, which was mitigated by ubiquinol with enhanced regeneration, goblet cells, and intestinal alkaline phosphatase expression. Compared to the irradiated group, the Ubq-treated groups had a significant recovery of intestinal interleukin-1β, caspase-3, nitric oxide metabolites, and thio-barbituric reactive substances to near-healthy levels. Ubq_Pre/Post group displayed elevated peroxisome proliferator-activated receptor (PPAR-γ) level, suggesting heightened benefits. Serum insulin reduction in irradiated rats improved post-Ubq treatment, with a possible anti-inflammatory effect on the pancreatic tissue. Fecal microbiota profiling revealed a dysbiosis state with a reduction of bacterial diversity post-irradiation, which was re-modulated in the Ubq treated groups to profiles that are indistinguishable from the control group. These findings underscore Ubq's gastroprotective effects against radiation-induced enteritis and its potential in restoring the gut microbiota’s diversity and balance. 

Abstract Members of the phylum Acidobacteriota inhabit a wide range of ecosystems including soils. We analyzed the global patterns of distribution and habitat preferences of various Acidobacteriota lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline, and terrestrial non-soil ecosystem) in 248,559 publicly available metagenomic datasets. Classes Terriglobia, Vicinamibacteria, Blastocatellia, and Thermoanaerobaculia were highly ubiquitous and showed clear preference to soil over non-soil habitats, class Polarisedimenticolia showed comparable ubiquity and preference between soil and non-soil habitats, while classes Aminicenantia and Holophagae showed preferences to non-soil habitats. However, while specific preferences were observed, most Acidobacteriota lineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of theAcidobacteriota. The observed lack of strong habitat specialization and habitat transition driven lineage evolution in the Acidobacteriota suggest ready cross colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment of Acidobacteriota as a major component in soil microbiomes post ecosystem disturbance events or during pedogenesis. 

Abstract Anaerobic gut fungi (AGF; Neocallimastigomycota) are crucial for the degradation of plant biomass in herbivores. While extensively studied in mammals, information regarding their occurrence, diversity, and community structure in nonmammalian hosts remains sparse. Here, we report on the AGF community in fecal samples of 13 domesticated ostriches. The ostrich (Struthio camelus) is an herbivorous, flightless, hindgut-fermenting member of the class Aves (birds). Illumina-based metabarcoding targeting the D2 region of the large ribosomal subunit (28S rRNA) revealed a uniform AGF community with low alpha diversity in the fecal samples. The community was mostly comprised of sequences potentially representing two novel species in the genus Piromyces, and a novel genus in the Neocallimastigomycota. Sequences affiliated with these novel taxa were absent or extremely rare in datasets derived from mammalian and tortoise samples, indicating a strong pattern of AGF-host association. One Piromyces strain (strain Ost1) was successfully isolated. Transcriptomics-enabled molecular dating analysis suggested a divergence time of ≈ 30Mya, a time frame in line with current estimates for ostrich evolution. Comparative gene content analysis between strain Ost1 and other Piromyces species from mammalian sources revealed a high degree of similarity. Our findings expand the range of AGF animal hosts to include members of the birds (class Aves), highlight a unique AGF community in the ostrich alimentary tract, and document the occurrence of a strong pattern of fungal–host association in ostriches, similar to previously observed patterns in AGF canonical mammalian hosts. 

Abstract Macronutrients play a vital role in host immunity and can influence host–pathogen dynamics, potentially through dietary effects on gut microbiota. To increase our understanding of how dietary macronutrients affect physiology and gut microbiota and investigate whether feeding behaviour is influenced by an immune threat, we conducted two experiments. First, we determined whether zebra finches (Taeniopygia guttata) exhibit shifts in physiology and gut microbiota when fed diets differing in macronutrient ratios. We found the type and amount of diet consumed affected gut microbiota alpha diversity, where microbial richness and Shannon diversity increased with caloric intake in birds fed a high‐fat diet and decreased with caloric intake in birds fed a high protein diet. Diet macronutrient content did not affect physiological metrics, but lower caloric intake was associated with higher complement activity. In our second experiment, we simulated an infection in birds using the bacterial endotoxin lipopolysaccharide (LPS) and quantified feeding behaviour in immune challenged and control individuals, as well as birds housed near either a control pair (no immune threat), or birds housed near a pair given an immune challenge with LPS (social cue of heightened infection risk). We also examined whether social cues of infection alter physiological responses relevant to responding to an immune threat, an effect that could be mediated through shifts in feeding behaviour. LPS induced a reduction in caloric intake driven by a decrease in protein, but not fat consumption. No evidence was found for socially induced shifts in feeding behaviour, physiology or gut microbiota. Our findings carry implications for host health, as sickness‐induced anorexia and diet‐induced shifts in the microbiome could shape host–pathogen interactions. 

ABSTRACT An enrichment of sulfidic sediments from Zodletone spring was sequenced as a metagenome. Draft genomes representing Cloacimonadota, Deltabacterota, Firmicutes, and Patescibacteria were binned and annotated and will aid functional genomics and cultivation efforts. 

ABSTRACT In the central plains of North America, the beetle family Silphidae comprised two subfamilies, Silphinae and Nicrophorinae, differentiated by reproductive behaviors. Silphinae, known as carrion beetles, feed on carrion and fly larvae and produce free-living larvae that receive no parental care. Adult Nicrophorinae, known as burying beetles, prepare a vertebrate carcass into a brood ball and provide biparental care to their offspring. Preparation of a brood ball involves coating the carcass in antimicrobial oral and anal secretions. These secretions contain a community of microbes, referred to as the secretion microbiome, which inhibit carcass microbe succession, preventing normal decomposition. Here, the secretion microbiomes of five species of Nicrophorinae and two species of Silphinae, both sampled from Oklahoma, with additional Nicrophorinae from Nebraska, were characterized using culture-independent analyses to understand and decipher factors shaping diversity and community structure. We identify the core secretion microbiome across Silphidae and show that, while the host subfamily, secretion type, and collection locality had no significant effect on the bacterial community alpha diversity, these factors significantly influenced bacterial community structure. Global and local tests of phylogenetic associations identified 14 genera with phylogenetic signals to the host subfamily and species. Description of the bacterial communities present in silphid secretions furthers our understanding of how these beetles interact with microbes for carcass nutrient processing. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials. IMPORTANCEThe manuscript explores the secretion bacterial community of carrion and burying beetles of the central plains of North America. A core secretion microbiome of 11 genera is identified. The host subfamily, secretion type, and collection locality significantly affects the secretion microbiome. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials. 

We report on the isolation and characterization of three isolates of anaerobic gut fungi from a cattle faecal sample obtained in Stillwater, OK, USA. The isolates produced polycentric thalli with nucleated rhizomycelia, lobed appressorium-like structures, intercalary sporangia and constricted sausage-like hyphae. These morphological features are characteristic of members of the genusAnaeromyces. No zoospore production was observed during the isolation process or thereafter. The strains seemed to have propagated solely through their nucleated hyphae post initial enrichment. Phylogenetic analysis of the D1/D2 region of the large ribosomal subunit (D1/D2 LSU) rRNA, the ribosomal intergenic spacer region 1 (ITS1), RNA polymerase II large subunit (RPB1) and comparative average amino acid identity using transcriptomic datasets further confirmed the position of the type strain as a distinct member of the genusAnaeromyces, familyAnaeromycetaceaeand phylumNeocallimastigomycota. We propose to accommodate these isolates into a new species (Anaeromyces corallioides) within the genusAnaeromyces. The type strain is EE.1.