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1. Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

   Solden LM; AE Naas; S Roux; RA Daly; WB Collins; CD Nicora; SO Purvine; DW Hoyt; J Schucke; B Jorgensen; et al (October 2018, Nature microbiology)

   NA- but there is a DOI 10.1038/s41564-018-0225-4 (Ed.)

   Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing access to rumen microbial communities actively degrading woody plant biomass in real time. We resolved 1,193 viral contigs and 77 unique, near-complete microbial metagenome-assembled genomes, many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique metagenome-assembled genomes, revealing a genome-resolved three tiered carbohydrate-fuelled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrated that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem. 

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2. Host-microbial interactions in the metabolism of different dietary fats

   https://doi.org/10.1016/j.cmet.2021.04.011  

   Chadaideh, Katia S; Carmody, Rachel N (May 2021, Cell metabolism)

   Although generally presumed to be isocaloric, dietary fats can differ in their energetic contributions and metabolic effects. Here, we show how an explicit consideration of the gut microbiome and its interactions with human physiology can enrich our understanding of dietary fat metabolism. We outline how variable human metabolic responses to different dietary fats, such as altered ileal digestibility or bile acid production, have downstream effects on the gut microbiome that differentially promote energy gain and inflammation. By incorporating host-microbial interactions into energetic models of human nutrition, we can achieve greater insight into the underlying mechanisms of diet-driven metabolic disease. 

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3. dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes

   https://doi.org/10.1093/nar/gkac1068  

   Zheng, Jinfang; Hu, Boyang; Zhang, Xinpeng; Ge, Qiwei; Yan, Yuchen; Akresi, Jerry; Piyush, Ved; Huang, Le; Yin, Yanbin (November 2022, Nucleic Acids Research)

   Abstract Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server. 

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4. Cloacal microbial diversity is associated with competitive phenotypes in socially polyandrous jacanas

   https://doi.org/10.1093/ornithology/ukaf031  

   Houtz, Jennifer L; Acosta, Kimberly A; Berlow, Mae; Lipshutz, Sara E (July 2025, Ornithology)

   The composition of host-associated microbial communities may correlate with the overall status of the host, including physiology and fitness. New bi-directional hypotheses suggest that sexual behaviors can shape, and be shaped by reproductive microbiomes, which may be particularly important for species with mating systems that feature strong sexual selection. These dynamics have been particularly understudied in female animals. Using 16S rRNA sequencing, we compared the cloacal microbiome of females and males from two socially polyandrous bird species that vary in the strength of sexual selection, Jacana spinosa (Northern Jacana) and J. jacana (Wattled Jacana). We hypothesized that the strength of sexual selection would shape cloacal microbial diversity, such that the more polyandrous J. spinosa would have a more diverse microbiome, and that microbiomes would be more diverse in females than in males. If the reproductive microbiome is indicative of competitive status, we also hypothesized that cloacal microbial diversity would be associated with competitive traits, including plasma testosterone levels, body mass, or weaponry. We found no differences in microbial alpha diversity between species or sexes, but we did find that microbial beta diversity significantly differed between species. We also found a positive relationship between microbial alpha diversity and testosterone in female J. spinosa. Future experiments are needed to explore the potential drivers of correlations between the cloacal microbiome and competitive phenotypes in socially polyandrous jacanas. 

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5. The buzz within: the role of the gut microbiome in honeybee social behavior

   https://doi.org/10.1242/jeb.246400  

   Nguyen, J B; Marshall, C W; Cook, C N (February 2024, Journal of Experimental Biology)

   ABSTRACT Gut symbionts influence the physiology and behavior of their host, but the extent to which these effects scale to social behaviors is an emerging area of research. The use of the western honeybee (Apis mellifera) as a model enables researchers to investigate the gut microbiome and behavior at several levels of social organization. Insight into gut microbial effects at the societal level is critical for our understanding of how involved microbial symbionts are in host biology. In this Commentary, we discuss recent findings in honeybee gut microbiome research and synthesize these with knowledge of the physiology and behavior of other model organisms to hypothesize how host–microbe interactions at the individual level could shape societal dynamics and evolution. 

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