Gut Microbiota Reveals the Environmental Adaption in Gastro-intestinal Tract of Wild Boar in Karst Region of Southwest China

BackgroundGut microbes, has become one of the research hotspots in animal ecology, playing an important role in monitoring dietary adaptation and health status of host. However, there are few studies on the gut microbiota in the stomach, small intestine (ileum) and large intestine (cecum, colon and rectum) of wild boar. ResultsAlpha diversity and Beta diversity showed there were significant differences in the abundance and distribution of microbes in gastrointestinal tract of wild boar. Firmicutes and Bacteroidetes were the most dominant phyla in stomach, cecum, colon and rectum of wild boar, while Proteobacteria and Firmicutes were the most dominant in ileum. At genus level, there were different leading genera in stomach (Prevotella and Lactobacillus), small intestine (Escherichia-Shigella and Lactobacillus) and large intestine (Ruminococcaceae_UCG-005, Christensenellaceae_R-7_group and Escherichia-Shigella). PICRUSt function predictive analysis suggested that there were significant differences in microbial metabolic pathways among five locations of wild boar. ConclusionsThis study comprehensively revealed the differences in composition of microbial community in gastrointestinal trac of wild boar. Future work links microbes with the metabolites to accurately reveal the health of wild boar.

Isotopic investigation of skeletal remains at the Imdang tombs reveals high consumption of game birds and social stratification in ancient Korea

Understanding the development of early states on the Korean Peninsula is an important topic in Korean archaeology. However, it is not clear how social structure was organized by these early states and what natural resources were utilized from their surrounding environments. To investigate dietary adaptation and social status in ancient Korea, stable isotope ratios and radiocarbon dates were measured from humans and animals from the Imdang cemetery, Gyeongsan city, South Korea. The results indicate that the Imdang diet was mainly based on C3 plants and terrestrial animals. Animal remains in the graves were directly consumed as daily food items as well as for ritual offerings. MixSIAR modeling results revealed that the dietary sources for the humans were: game birds > C3 plants > terrestrial herbivores > marine fish > C4 plants. The finding that the game birds represented the highest contribution to the whole diet, indicates that game birds must have been intensively hunted. Furthermore, elites consumed more game birds than their retainers and they also consumed seafood as a privileged dietary item in the Imdang society. This study demonstrates that the Apdok was a stratified society having high variations in the consumption of food items available to an individual and provides new insights about the subsistence and social status of the early ancient Apdok state on the Korean Peninsula.

Dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation

Dietary adaptation is the acquisition of an efficient system to digest food available in an ecosystem. To find the genetic basis for human dietary adaptation, we searched 16 genomes from Neandertal, Denisovan and Early Sapiens for food digestion genes that tend to have more or fewer copies than the modern human reference genome. Here, we identify 11 genes, including three gene clusters, with discernible copy number variation trends at the population level. The genomic variation shows how metabolic pathways for lipid, brown fat, protein or carbohydrate metabolism adapt to metabolize food from animal or plant sources. Interpreting the copy number profiles in relation to fossil evidence shows that Homo sapiens had an evolutionary advantage compared to Neandertal and Denisovan in adapting to cold and temperate ecosystems.

Impacts of bunk management on steer performance and ruminal hydrogen sulfide concentrations in steers fed modified distillers grains with solubles

Two experiments were conducted to evaluate the impacts of bunk management on dry matter intake (DMI), growth performance, carcass characteristic, and hydrogen sulfide (H2S) concentrations in beef steers fed modified distillers grains with solubles (MDGS; DM basis). In Experiment 1, 139 steers (440.4 ± 31.0 kg) were randomly assigned to one of 16 pens with pen randomly assigned to one of two treatments: 1) Control (CON, bunks managed to be devoid of feed prior to feeding), or 2) Over-fed (OVF, bunks managed to have minimum of 2.54 cm of feed remaining each morning) during adaptation. Following adaptation all steers in experiment 1 were transitioned to CON bunks and followed to finishing. In Experiment 2, 126 steers (445.4 ± 40.63 kg) were randomly assigned to one of 16 pens. Treatments in Experiment 2 were arranged in a 2 × 2 factorial and include the two bunk management strategies utilized in Experiment 1 (OVF or CON) and either 25% MDGS or 50% MDGS (DM basis). Ruminal H2S was measured via rumenocentesis during dietary adaptation. There were no differences (P ≥ 0.13) observed in either experiment for growth performance due to bunk management. In Experiment 1, OVF steers had greater (P = 0.001) DMI during adaptation; however, overall DMI was not different (P = 0.14) between treatments. In Experiment 2, DMI (d 0 to 104) tended to decrease (P = 0.09) with greater MDGS inclusion. Hot carcass weight, ribeye area, marbling score and quality grade were not affected (P ≥ 0.48) by either bunk management or MDGS inclusion. In Experiment 2, back fat (1.30 versus 1.17 ± 0.042 cm) and yield grade (3.2 versus 3.0 ± 0.11) were greater (P = 0.03) for CON steers compared to OVF but were not affected (P = 0.59) by MDGS inclusion. In Experiment 1, H2S tended (P = 0.07) to be greater in steers on OVF compared to CON. In Experiment 2, bunk management strategy did not impact (P = 0.82) H2S concentrations. There was a MDGS inclusion × day interaction for H2S with steers fed 50% MDGS having greater (P < 0.01) H2S concentrations compared to steers fed 25% MDGS on days 28 and 35. Bunk management strategy during adaptation did not impact growth performance but did reduce intake in Experiment 1. Yield grade decreased when OVF bunk management was applied throughout Experiment 2. Response of hydrogen sulfide concentrations in the rumen were variable and likely influenced by inconsistencies in bunk management and resulting DMI during the early portions of the feedlot study.

Molecular Evolution of Tooth-Related Genes Provides New Insights into Dietary Adaptations of Mammals

Mammals have evolved different tooth phenotypes that are hypothesized to be associated with feeding habits. However, the genetic basis for the linkage has not been well explored. In this study, we investigated 13 tooth-related genes, including seven enamel-related genes (AMELX, AMBN, ENAM, AMTN, ODAM, KLK4 and MMP20) and six dentin-related genes (DSPP, COL1A1, DMP1, IBSP, MEPE and SPP1), from 63 mammals to determine their evolutionary history. Our results showed that different evolutionary histories have evolved among divergent feeding habits in mammals. There was stronger positive selection for eight genes (ENAM, AMTN, ODAM, KLK4, DSPP, DMP1, COL1A1, MEPE) in herbivore lineages. In addition, AMELX, AMBN, ENAM, AMTN, MMP20 and COL1A1 underwent accelerated evolution in herbivores. While relatively strong positive selection was detected in IBSP, SPP1, and DSPP, accelerated evolution was only detected for MEPE and SPP1 genes among the carnivorous lineages. We found positive selection on AMBN and ENAM genes for omnivorous primates in the catarrhini clade. Interestingly, a significantly positive association between the evolutionary rate of ENAM, ODAM, KLK4, MMP20 and the average enamel thickness was found in primates. Additionally, we found molecular convergence in some amino acid sites of tooth-related genes among the lineages whose feeding habit are similar. The positive selection of related genes might promote the formation and bio-mineralization of tooth enamel and dentin, which would make the tooth structure stronger. Our results revealed that mammalian tooth-related genes have experienced variable evolutionary histories, which provide some new insights into the molecular basis of dietary adaptation in mammals.

Asymmetric expression of homoeologous genes contributes to dietary adaption of an allodiploid hybrid fish derived from Megalobrama amblycephala (♀) × Culter alburnus (♂)

Background Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with one another in a single nucleus, which may cause subgenome interaction and dominance at the gene expression level and has been observed in some allopolyploid plants. In our previous studies, newly formed allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) had herbivorous characteristic. It is thus interesting to further characterize whether the subgenome interaction and dominance derive dietary adaptation of this hybrid fish. Results Differential expression, homoeolog expression silencing and bias were investigated in the hybrid fish after 70 days of adaptation to carnivorous and herbivorous diets. A total of 2.65 × 108 clean reads (74.06 Gb) from the liver and intestinal transcriptomes were mapped to the two parent genomes based on specific SNPs. A total of 2538 and 4385 differentially expressed homoeologous genes (DEHs) were identified in the liver and intestinal tissues between the two groups of fish, respectively, and these DEHs were highly enriched in fat digestion and carbon metabolism, amino acid metabolism and steroid biosynthesis. Furthermore, subgenome dominance were observed in tissues, with paternal subgenome was more dominant than maternal subgenome. Moreover, subgenome expression dominance controlled functional pathways in metabolism, disease, cellular processes, environment and genetic information processing during the two dietary adaptation processes. In addition, few but sturdy villi in the intestine, significant fat accumulation and a higher concentration of malondialdehyde in the liver were observed in fish fed carnivorous diet compared with fish fed herbivorous diet. Conclusions Our results indicated that diet drives phenotypic and genetic variation, and the asymmetric expression of homoeologous genes (including differential expression, expression silencing and bias) may play key roles in dietary adaptation of hybrid fish. Subgenome expression dominance may contribute to uncovering the mechanistic basis of heterosis and also provide perspectives for fish genetic breeding and application.

Reconstructing dietary ecology of extinct strepsirrhines (Primates, Mammalia) with new approaches for characterizing and analyzing tooth shape

The morphological and ecological diversity of lemurs and lorisiformes once rivaled that of the rest of the primate order. Here, we assemble a dataset of 3D models representing the second mandibular molars of a wide range of extant and fossil strepsirrhines encompassing this diversity. We use these models to distill quantitative descriptors of tooth form and then analyze these data using new analytical methods. We employ a recently developed dental topography metric (ariaDNE), which is less sensitive to details of random error in 3D model quality than previously used metrics (e.g., DNE); Bayesian multinomial modeling with metrics designed to measure overfitting risk; and a tooth segmentation algorithm that allows the shapes of disaggregated tooth surface features to be quantified using dental topography metrics. This approach is successful at reclassifying extant strepsirrhine primates to known dietary ecology and indicates that the averaging of morphological information across the tooth surface does not interfere with the ability of dental topography metrics to predict dietary adaptation. When the most informative combination of dental topography metrics is applied to extinct species, many subfossil lemurs and the most basal fossil strepsirrhines are predicted to have been primarily frugivorous or gummivorous. This supports an ecological contraction among the extant lemurs and the importance of frugivory in the origins of crown Strepsirrhini, potentially to avoid competition with more insectivorous and folivorous members of Paleogene Afro-Arabian primate faunas.

Dietary habits of free-ranging banded langur (Presbytis femoralis) in a secondary-human modified forest in Johor, Malaysia

ABSTRACTBanded langurs, Presbytis femoralis, are distributed in southern Peninsular Malaysia, i.e., Johor and its borders including Singapore. It has been estimated that there are only < 250 mature individuals of P. femoralis in Malaysia and Singapore, and it is currently assessed as Critically Endangered. The dietary information of P. femoralis and even other closely related species has rarely been reported. This study, therefore, aimed to describe their dietary habits and discuss interaction between their feeding behaviour and its surrounding. This study was conducted from February to November 2018, with 15 sampling days each month. We collected a total of 186 sighting hours, using a scan sampling method with 10-min intervals, on a five-langur focal group. We have identified 29 species with 47 items consumed by the banded langur, mostly young leaves (51 %) followed by fruits (45 %), and flowers (3.8 %). The study group spent slightly more time consuming non-cultivated plants but relied on cultivated plants for the fruits. Over 75% of fruit feeding involved consuming cultivar plants; in most cases (73%), they ate only the pule, not the seeds. Since the cultivated plants was planted in human settlement, there is an urgent need to implement conservation measures to untangle the human-langur conflicts for instance, reforestation of a buffer region using non-cultivated plants. There is a potential for building upon our new findings with more detailed investigations, such as more extensive ecological factors influencing the dietary adaptation which would be necessary to support conservation efforts and management decisions of this species.

Transcriptomics Unravels Molecular Players Shaping Dorsal Lip Hypertrophy in the Vacuum Cleaner Cichlid, Gnathochromis Permaxillaris

Background:Teleosts display a spectacular diversity of craniofacial adaptations that often mediate ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniofacial morphologies, but less is known about soft craniofacial phenotypes. Here we focus on a bizarre example of lip hypertrophy in the Lake Tangnayika cichlid, Gnathochromis permaxillaris, that is considered to be a dietary adaptation to suck invertebrates out of narrow crevices. In this study, we investigate the molecular and regulatory basis of lip development G. permaxillaris, using a comparative transcriptomic approach.Results: We identified a gene regulatory network involved in tissue overgrowth and cellular hypertrophy, potentially associated with the formation of a locally restricted hypertrophic lip in a teleost fish species. Of particular interest were the increased expression level of apoda and fhl2, as well as reduced expression of cyp1a, gimap8, lama5 and rasal3, in the hypertrophic lip region which have been implicated in formation of lip structure in other vertebrates. Among the predicted upstream transcription factors, we found reduced expression foxp1 in the hypertrophic lip region, which is known to act as repressor of cell growth and proliferation and its function has been associated with hypertrophy of upper lip in human. Conclusion: Our results provide a genetic foundation for future studies of molecular players shaping soft and exaggerated, but locally restricted, craniofacial morphological changes in fish and perhaps across vertebrates.