scholarly journals Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies

2015 ◽  
Vol 6 ◽  
Author(s):  
Mario Carrillo-Araujo ◽  
Neslihan TaÅŸ ◽  
Rocio J. Alcántara-Hernández ◽  
Osiris Gaona ◽  
Jorge E. Schondube ◽  
...  
Keyword(s):  
Feeding Strategies ◽  
Microbiome Composition ◽  
Host Phylogeny

Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats (Neotoma spp.)

2021 ◽  
Vol 118 (47) ◽  
pp. e2108787118
Author(s):  
Sara B. Weinstein ◽  
Rodolfo Martínez-Mota ◽  
Tess E. Stapleton ◽  
Dylan M. Klure ◽  
Robert Greenhalgh ◽  
...  
Keyword(s):  
Structure And Stability ◽  
Microbiome Composition ◽  
Ecological Selection ◽  
Microbiome Diversity ◽  
In Captivity ◽  
Host Phylogeny ◽  
Host Genetic ◽  
Microbial Symbionts ◽  
Species Specific ◽  
Symbiotic Community

The microbiome is critical for host survival and fitness, but gaps remain in our understanding of how this symbiotic community is structured. Despite evidence that related hosts often harbor similar bacterial communities, it is unclear whether this pattern is due to genetic similarities between hosts or to common ecological selection pressures. Here, using herbivorous rodents in the genus Neotoma, we quantify how geography, diet, and host genetics, alongside neutral processes, influence microbiome structure and stability under natural and captive conditions. Using bacterial and plant metabarcoding, we first characterized dietary and microbiome compositions for animals from 25 populations, representing seven species from 19 sites across the southwestern United States. We then brought wild animals into captivity, reducing the influence of environmental variation. In nature, geography, diet, and phylogeny collectively explained ∼50% of observed microbiome variation. Diet and microbiome diversity were correlated, with different toxin-enriched diets selecting for distinct microbial symbionts. Although diet and geography influenced natural microbiome structure, the effects of host phylogeny were stronger for both wild and captive animals. In captivity, gut microbiomes were altered; however, responses were species specific, indicating again that host genetic background is the most significant predictor of microbiome composition and stability. In captivity, diet effects declined and the effects of host genetic similarity increased. By bridging a critical divide between studies in wild and captive animals, this work underscores the extent to which genetics shape microbiome structure and stability in closely related hosts.

scholarly journals Daily feeding rhythm linked to microbiome composition in two zooplankton species

2021 ◽  
Author(s):  
Alaina C Pfenning-Butterworth ◽  
Reilly Cooper ◽  
Clay Cressler
Keyword(s):  
Feeding Behavior ◽  
Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Daily Feeding ◽  
Microbiome Diversity ◽  
Rrna Sequencing ◽  
Host Phylogeny ◽  
Induced Changes

Host-associated microbial communities are impacted by external and within-host factors, i.e., diet and feeding behavior. For organisms known to have a circadian rhythm in feeding behavior, microbiome composition is likely impacted by the different rates of microbe introduction and removal across a daily cycle, in addition to any diet-induced changes in microbial interactions. Here, we measured feeding behavior and used 16S rRNA sequencing to compare the microbial community across a diel cycle in two distantly related species of Daphnia, that differ in their life history traits, to assess how daily feeding patterns impact microbiome composition. We find that Daphnia species reared under similar laboratory conditions have significantly different microbial communities. Additionally, we reveal that Daphnia have daily differences in their microbial composition that correspond with feeding behavior, such that there is greater microbiome diversity at night during the host's active feeding phase. These results highlight that zooplankton microbiomes are relatively distinct and are likely influenced by host phylogeny.

scholarly journals Diet Modification and Not Timed Feeding Strategies Result in Intestinal Microbiome Alterations (P21-030-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Marie van der Merwe ◽  
Sunita Sharma ◽  
Jade Caldwell ◽  
Nicholas Smith ◽  
Richard Bloomer ◽  
...  
Keyword(s):  
High Fat Diet ◽  
Beta Diversity ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
Intestinal Microbiome ◽  
Feeding Strategies ◽  
High Fat ◽  
Microbiome Composition ◽  
Intestinal Length

Abstract Objectives Time-restricted feeding strategies have been shown to normalize obesity parameters, even under high fat feeding conditions. The objective of this study is to examine whether timed feeding alters parameters of gut health or intestinal microbiome composition. Methods C57BL/6 male mice were randomized to Chow or a high fat diet (HFD) for 6 weeks, followed by a switch from HFD to 1) Chow (sChow), 2) Purified Vegan – Daniel Fast (DF), 3) HFD ad lib, 4) HFD time restricted (TRF), 5) HFD alternative day fasting (ADF), or 6) HFD 60% caloric restriction (CR) for an additional 8 weeks. Results We observed that body mass gain was reduced for all intervention groups (P ≤ 0.0001). Small intestinal length and cecal weight were increased in Chow, sChow and DF (P ≤ 0.02), while total cecal short chain fatty acid (SCFA) concentration was non-significantly increased for all groups consuming the HFD. Proprionate was specifically increased in the Chow, sChow and DF groups (P ≤ 0.02). Chow fed microbiota remained stable in taxonomic composition and alpha diversity (Shannon diversity index) throughout the study. HF fed microbiota displayed lower alpha diversity along with reduced phylum levels of Bacteroidetes and increase Firmicutes. Animals switched from HF to Chow demonstrated a rapid transition in taxonomic composition, alpha, and beta diversity that initially resembled HF, but clustered closely with Chow by weeks 4 and 8 of intervention. After 8 weeks on the respective dietary protocols, alpha diversity of the DF was most similar to Chow fed animals and also resulted in the largest increase in Bacteriodetes and largest decrease in Firmicutes. Beta diversity (weighted UniFrac) showed Chow, sChow, and DF clustered together, while high fat fed groups (HF, CR, ADF, and TRF) clustered. Compared with HF controls, CR and TRF led to a relative increase in the classes Clostridia, Deferribacteres and Deltaproteobacteria. The taxonomic composition and alpha diversity of ADF fasting resembled HF under fed conditions, while ADF under fasting conditions more closely resembled CR and TRF. Conclusions In conclusion, timed feeding on a high fat diet did not result in significant changes in the microbiome, demonstrating that diet, and not fasting is the major determinant for microbiome composition. Funding Sources University of Memphis & Children's Foundation Research Institute, Memphis.

scholarly journals Phylosymbiosis across Deeply Diverging Lineages of Omnivorous Cockroaches (Order Blattodea)

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Kara A. Tinker ◽  
Elizabeth A. Ottesen
Keyword(s):  
Gut Microbiota ◽  
Significant Role ◽  
Gut Microbiome ◽  
Host Species ◽  
Evolutionary Divergence ◽  
Phylogenetic Distance ◽  
Evolutionary Time ◽  
Microbiome Composition ◽  
Ancient Lineage ◽  
Host Phylogeny

ABSTRACT The gut microbiome is shaped by both host diet and host phylogeny. However, separating the relative influence of these two factors over long periods of evolutionary time is often difficult. We conducted a 16S rRNA gene amplicon-based survey of the gut microbiome from 237 individuals and 19 species of omnivorous cockroaches from the order Blattodea. The order Blattodea represents an ancient lineage of insects that emerged over 300 million years ago, have a diverse gut microbiota, and have a typically gregarious lifestyle. All cockroaches shared a broadly similar gut microbiota, with 66 microbial families present across all species and 13 present in every individual examined. Although our network analysis of the cockroach gut microbiome showed a large amount of connectivity, we demonstrated that gut microbiota cluster strongly by host species. We conducted follow-up tests to determine if cockroaches exhibit phylosymbiosis, or the tendency of host-associated microbial communities to parallel the phylogeny of related host species. Across the full data set, gut microbial community similarity was not found to correlate with host phylogenetic distance. However, a weak but significant phylosymbiotic signature was observed using the matching cluster metric, which allows for localized changes within a phylogenetic tree that are more likely to occur over long evolutionary distances. This finding suggests that host phylogeny plays a large role in structuring the cockroach gut microbiome over shorter evolutionary distances and a weak but significant role in shaping the gut microbiome over extended periods of evolutionary time. IMPORTANCE The gut microbiome plays a key role in host health. Therefore, it is important to understand the evolution of the gut microbiota and how it impacts, and is impacted by, host evolution. In this study, we explore the relationship between host phylogeny and gut microbiome composition in omnivorous, gregarious cockroaches within the Blattodea order, an ancient lineage that spans 300 million years of evolutionary divergence. We demonstrate a strong relationship between host species identity and gut microbiome composition and found a weaker but significant role for host phylogeny in determining microbiome similarity over extended periods of evolutionary time. This study advances our understanding of the role of host phylogeny in shaping the gut microbiome over different evolutionary distances.

scholarly journals Intestinal microbes: an axis of functional diversity among large marine consumers

2020 ◽  
Vol 287 (1924) ◽  
pp. 20192367
Author(s):  
Jarrod J. Scott ◽  
Thomas C. Adam ◽  
Alain Duran ◽  
Deron E. Burkepile ◽  
Douglas B. Rasher
Keyword(s):  
Feeding Behaviour ◽  
Functional Trait ◽  
Intestinal Microbiome ◽  
Herbivorous Fishes ◽  
Intestinal Microbes ◽  
Microbiome Composition ◽  
Phylogenetic Comparison ◽  
Coral Reef Resilience ◽  
Host Phylogeny ◽  
Species Specific

Microbes are ubiquitous throughout the world's oceans, yet the manner and extent of their influence on the ecology and evolution of large, mobile fauna remains poorly understood. Here, we establish the intestinal microbiome as a hidden, and potentially important, ‘functional trait’ of tropical herbivorous fishes—a group of large consumers critical to coral reef resilience. Using field observations, we demonstrate that five common Caribbean fish species display marked differences in where they feed and what they feed on. However, in addition to space use and feeding behaviour—two commonly measured functional traits—we find that interspecific trait differences are even more pronounced when considering the herbivore intestinal microbiome. Microbiome composition was highly species specific. Phylogenetic comparison of the dominant microbiome members to all known microbial taxa suggest that microbiomes are comprised of putative environmental generalists, animal-associates and fish specialists (resident symbionts), the latter of which mapped onto host phylogeny. These putative symbionts are most similar to—among all known microbes—those that occupy the intestines of ecologically and evolutionarily related herbivorous fishes in more distant ocean basins. Our findings therefore suggest that the intestinal microbiome may be an important functional trait among these large-bodied consumers.

scholarly journals No evidence for phylosymbiosis in western chipmunk species

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Kirsten Grond ◽  
Kayce C Bell ◽  
John R Demboski ◽  
Malia Santos ◽  
Jack M Sullivan ◽  
...  
Keyword(s):  
Sampling Site ◽  
Geographic Distance ◽  
Nuclear Genome ◽  
Local Environment ◽  
Ecological Niches ◽  
Isolated Populations ◽  
Wild Mammals ◽  
Microbiome Composition ◽  
Host Phylogeny ◽  
Future Work

ABSTRACT Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: (1) increasing host mitochondrial relatedness, (2) increasing host nuclear genome relatedness and (3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.

scholarly journals Host Phylogeny and Diet Shape Gut Microbial Communities Within Bamboo-Feeding Insects

2021 ◽  
Vol 12 ◽  
Author(s):  
Kuanguan Huang ◽  
Jie Wang ◽  
Junhao Huang ◽  
Shouke Zhang ◽  
Alfried P. Vogler ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Future Research ◽  
Feeding Strategies ◽  
Sequencing Platform ◽  
Diet Specialization ◽  
Dietary Niche ◽  
Host Phylogeny ◽  
Specialized Diet

The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we profiled the microbial communities of 76 gut samples collected from nine bamboo-feeding insects, including both hemimetabolous (Orthoptera and Hemiptera) and holometabolous (Coleoptera and Lepidoptera) species, which are specialized in three distinct dietary niches: bamboo leaf, shoot, and sap. The gut microbiota of these insects were dominated by Proteobacteria, Firmicutes, and Bacteroidetes and were clustered into solid (leaf and shoot) and liquid (sap) dietary niches. The gut bacterial communities of insects feeding on solid diet overlapped significantly, even though these insects belong to phylogenetically distant lineages representing different orders. In addition, the presence of cellulolytic bacterial communities within the gut microbiota allows bamboo-feeding insects to adapt to a highly specialized, fiber-rich diet. Although both phylogeny and diet can impact the structure and composition of gut microbiomes, phylogeny is the primary driving force underlying the convergent adaptation to a highly specialized diet, especially when the related insect species harbor similar gut microbiomes and share the same dietary niche over evolutionary timescales. These combined findings lay the foundation for future research on how convergent feeding strategies impact the interplays between hosts and their gut microbiomes and how the gut microbiota may facilitate convergent evolution in phylogenetically distant species in adaptation to the shared diet.

scholarly journals Mammalian gut metabolomes mirror microbiome composition and host phylogeny

2021 ◽  
Author(s):  
Rachel Gregor ◽  
Maraike Probst ◽  
Stav Eyal ◽  
Alexander Aksenov ◽  
Goor Sasson ◽  
...  
Keyword(s):  
Animal Species ◽  
Mammalian Species ◽  
Short Chain Fatty Acids ◽  
Taxonomic Composition ◽  
Mammalian Host ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Microbiome Composition ◽  
Host Phylogeny ◽  
Functionally Diverse

AbstractIn the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.

Profitability of dairy farming in relation to the type of feeding system

2011 ◽  
Vol 28 (1) ◽  
pp. 55-59 ◽  
Author(s):  
Jan Frelich ◽  
Martin Šlachta ◽  
František Střeleček ◽  
Jana Lososová
Keyword(s):  
Arable Land ◽  
Principal Component ◽  
Dairy Farming ◽  
Plant Production ◽  
Feeding Strategies ◽  
Feeding System ◽  
Financial Health ◽  
Profit Rate ◽  
Permanent Housing ◽  
Cow Performance

Profitability of dairy farming in relation to the type of feeding systemWe investigated the profitability of dairy farms in relation to the type of feeding system (seasonal pasture vs. permanent housing). An economic analysis was carried out of data on the structure and financial health of 50 farms in 2007 using questionnaires filled in by the farmers. The Principal Component Analysis (PCA) was applied to reveal causal relationships between a number of characteristics of the farms. The two axis of PCA explained 40.48% and 16.13% of the variability among the selected farm characteristics. Profitability related more to the number of subsidies, the area of arable land, the number of livestock and to the milk and plant production than to the area of meadows and pastures. Although a better cow performance was achieved on farms with confined herds, the profit per agricultural area and profit rate did not differ significantly between the two feeding strategies (P>0.05). The profit was 3,259 and 3,655 CZK/ha on average and the profit rate 7.9% and 5.6% on average on farms with pastured herds and on farms with confined herds, respectively. A lowering of input costs and a more effective utilisation of grasslands may further enhance profitability.

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