Ecological physiology of diet and digestive systems

Does intestine length explain digesta retention times in birds and mammals?

Previous studies have indicated that across birds and mammals, body mass is a comparatively poor predictor of the time digesta is retained in the digestive tract (mean retention time, MRT). Rather, MRT might be determined by gastrointestinal anatomy, which can differ considerably within and between trophic guilds. Here, we used two recent literature compilations on the intestine length and the MRT in birds (n = 33 species) and mammals (n = 149) and applied comparative statistical approaches to assess whether intestine length is more closely correlated with MRT than body mass. Regardless of the statistical model used, whether small species (< 120 g and any larger bats) were included or not, or whether birds and mammals were assessed together or separately, intestinal length generally yielded a better model fit to MRT than body mass, supporting the general concept. Nevertheless, data scatter was substantial, indicating that intestine length, though better than body mass, is still a limited explanatory factor for MRT. The intestine length-MRT relationship is an example of the direct statistical assessment of a generally presumed form-function relationship that is typically represented as a narrative. In the comparative literature, such assessments are rare.

A conserved bacterial genetic basis for commensal-host specificity

Animals selectively acquire specific symbiotic gut bacteria from their environments that aid host fitness. To colonize, a symbiont must locate its niche and sustain growth within the gut. Adhesins are bacterial cell surface proteins that facilitate attachment to host tissues and are often virulence factors for opportunistic pathogens. However, the attachments are often transient and nonspecific, and additional mechanisms are required to sustain infection. In this work, we use live imaging of individual symbiotic bacterial cells colonizing the gut of living Drosophila melanogaster to show that Lactiplantibacillus plantarum specifically recognizes the fruit fly foregut as a distinct physical niche. L. plantarum establishes stably within its niche through host-specific adhesins encoded by genes carried on a colonization island. The adhesin binding domains are conserved throughout the Lactobacillales, and the island also encodes a secretion system widely conserved among commensal and pathogenic bacteria.

Transcriptional and physiological plasticity of the green peach aphid (Hemiptera: Aphididae) to cabbage and pepper plants

Defensive metabolites and nutrient restriction of host plants are 2 major obstacles to the colonization of insect herbivores. The green peach aphid (GPA) Myzus persicae (Sulzer) broadly colonizes plants with diverse nutritional and defensive traits. However, how GPA adapts to nutritional and defensive traits within different plants remains largely unknown. To elucidate this, we first investigated the performances and transcriptomes of GPA feeding on cabbage Brassica oleracea and pepper Capsicum annuum. The green peach aphid had lower weight and fecundity when feeding on cabbage than on pepper. The transcriptomic analysis found 824 differentially expressed genes (DEGs), and 13 of the top 20 Kyoto Encyclopedia of Genes and Genomes pathways are related to nutrient metabolism, energy metabolism, and detoxification. Specifically, we found 160 DEGs associated with the metabolism of protein and amino acids, sugar and lipids, and xenobiotic substances, 86 upregulated in cabbage-fed GPA. Fourteen cathepsin B genes were strongly upregulated in cabbage-fed GPA, and were enriched in lysosome pathway and 2 dominated gene ontology terms peptidase activity and proteolysis. In addition, cabbage-fed GPA upregulated sugar and lipid digestion, while downregulated lipid biosynthesis processes. Furthermore, 55 metabolic detoxification enzyme genes were differentially expressed between GPA on 2 hosts, and detoxification enzyme activities of GPA indeed changed accordingly to the host. Then, we found that cabbage has lower amino acids nutrition quality for GPA compared to pepper. Our results suggested that adjustment of nitrogen nutrient metabolism, sugar and lipid metabolism, and metabolic detoxification in a host-specific manner play crucial roles in the adaptations of GPA to different host plants.

A novel clinically relevant human fecal microbial transplantation model in humanized mice

The intact immune system of mice exhibits resistance to colonization by exogenous microorganisms, but the gut microbiota profiles of the humanized mice and the patterns of human fecal microbiota colonization remain unexplored. Humanized NCG (huNCG) mice were constructed by injected CD34 +stem cells. 16S rRNA sequencing and fecal microbiota transplantation (FMT) technologies were used to detect the differences in microbiota and selective colonization ability for exogenous community colonization among three mice cohorts (C57BL/6J, NCG, and huNCG). Flow cytometry analysis showed that all huNCG mice had over 25% hCD45 +in peripheral blood. 16S rRNA gene sequence analysis showed that compared with NCG mice, the gut microbiota of huNCG mice were significantly altered. After FMT, the principal coordinates analysis (PCoA) showed that the gut microbial composition of huNCG mice (huNCG-D9) was similar to that of donors. The relative abundance of Firmicutes and Bacteroidetes were significantly increased in huNCG mice compared to NCG mice. Further comparison of ASV sequences revealed that Bacteroides plebeius, Bacteroides finegoldii, Escherichia fergusonii, Escherichia albertii, Klebsiella pneumoniae, and Klebsiella variicola exhibited higher abundance and stability in huNCG mice after FMT. Furthermore, PICRUSt2 analysis showed that huNCG mice had significantly enhanced metabolism and immunity. This study demonstrated that humanized mice are more conducive to colonization within the human gut microbiota, which provides a good method for studying the association between human diseases and microbiota.IMPORTANCEThe gut microbiota and biomarkers of humanized mice are systematically revealed for the first time. The finding that human fecal microbiota colonize humanized mice more stably provides new insights into the study of interactions between immune responses and gut microbiota.

Unveiling symbiotic bacterial communities in insects feeding on the latex-rich plant Ficus microcarpa

The diversity and health of insects that feed on plants are closely related to their mutualistic symbionts and host plants. These symbiotic partners significantly influence various metabolic activities in these insects. However, the symbiotic bacterial community of toxic plant feeders still needs further characterisation. This study aims to unravel bacterial communities associated with the different species of insect representing three insect orders: Thysanoptera, Hemiptera, and Lepidoptera, along with their predicted functional role, which exclusively feeds on latex-rich plant species Ficus microcarpa. By using 16S rRNA gene high-throughput sequencing, the analysis was able to define the major alignment of the bacterial population, primarily comprising Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota. Significant differences in symbiotic organisms between three insect groups were discovered by the study: hemipterans had Burkholderia and Buchnera, and lepidopterans had Acinetobacter. At the same time, Pseudomonas was detected in high abundance in both lepidopteran and thysanopteran insects. Furthermore, these symbionts exhibit consistent core functions, potentially explaining how different insects can consume the same host plant. The identified core functions of symbionts open avenues for innovative approaches in utilising these relationships to develop environment-friendly solutions for pest control, with broader implications for agriculture and environmental conservation.

Digestive Enzyme Activities in Mussel Mytilus californianus Endure Acute Heat Exposure in Air

The mussel Mytilus californianus is an ecosystem engineer forming beds along the coastlines of Northeastern Pacific shores. As sessile organisms, they modulate their energy balance through valve movements, feeding, and digestive functionality. A recent study observed that activity of the digestive enzyme cellulase was higher than predicted in mussels high on the shore, where temperatures are characteristically high and food availability is limited compared to low-shore habitats. In the current study, we predicted that this scavenging behavior is induced to mitigate energy losses related to heat-shock responses-that cellulase and amylase will display hyperactivity for limited recourses in the face of aerial heating. In the laboratory, we acclimated mussels to three complex diets that differed in starch and cellulose composition, followed by two acute heat shocks (+8°C) in the laboratory. Results showed no hyperactivity of amylase and cellulase in heated mussels. These results differ from previous studies that showed lowered amylase activity following heat acclimation. This difference in amylase activity across heat-stress exposure time is important when analyzing mussel bed disturbances following heat waves that compromise energy balance or cause death within adult populations.

Response of growth and physiological enzyme activities in Eriogyna pyretorum to various host plants

Morphological attributes and chemical composition of host plants shape growth and development of phytophagous insects via influences on their behavior and physiological processes. This research delves into the relationship between Eriogyna pyretorum and various host plants through studuying how feeding on different host tree species affect growth, development, and physiological enzyme activities. We examined E. pyretorum response to three distinct host plants: Camphora officinarum, Liquidambar formosana and Pterocarya stenoptera. Notably, larvae feeding on C. officinarum and L. formosana displayed accelerated development, increased pupal length, and higher survival rates compared to those on P. stenoptera. This underlines the pivotal role of host plant selection in shaping the E. pyretorum's life cycle. The activities of a-amylase, lipase and protective enzymes were the highest in larvae fed on the most suitable host L. formosana which indicated that the increase of these enzyme activities was closely related to growth and development. Furthermore, our investigation revealed a relationship between enzymatic activities and host plants. Digestive enzymes, protective enzymes, and detoxifying enzymes exhibited substantial variations contingent upon the ingested host plant. Moreover, the total phenolics content in the host plant leaves manifested a noteworthy positive correlation with catalase and lipase activities. In contrast, a marked negative correlation emerged with glutathione S-transferase and α-amylase activities. The total developmental duration of larvae exhibited a significant positive correlation with the activities of GST and CarE. The survival rate of larvae showed a significant positive correlation with CYP450. These observations underscore the insect's remarkable adaptability in orchestrating metabolic processes in accordance with available nutritional resources. This study highlights the interplay between E. pyretorum and its host plants, offering novel insights into how different vegetation types influence growth, development, and physiological responses. These findings contribute to a deeper comprehension of insect-plant interactions, with potential applications in pest management and ecological conservation.

Chewing through challenges: Exploring the evolutionary pathways to wood-feeding in insects

Decaying wood, while an abundant and stable resource, presents considerable nutritional challenges due to its structural rigidity, chemical recalcitrance, and low nitrogen content. Despite these challenges, certain insect lineages have successfully evolved saproxylophagy (consuming and deriving sustenance from decaying wood), impacting nutrient recycling in ecosystems and carbon sequestration dynamics. This study explores the uneven phylogenetic distribution of saproxylophagy across insects and delves into the evolutionary origins of this trait in disparate insect orders. Employing a comprehensive analysis of gut microbiome data, from both saproxylophagous insects and their non-saproxylophagous relatives, including new data from unexplored wood-feeding insects, this Hypothesis paper discusses the broader phylogenetic context and potential adaptations necessary for this dietary specialization. The study proposes the "Detritivore-First Hypothesis," suggesting an evolutionary pathway to saproxylophagy through detritivory, and highlights the critical role of symbiotic gut microbiomes in the digestion of decaying wood.

Diet and habitat as determinants of intestine length in fishes

Fish biologists have long assumed a link between intestinal length and diet, and relative gut length or Zihler's index are often used to classify species into trophic groups. This has been done for specific fish taxa or specific ecosystems, but not for a global fish dataset. Here, we assess these relationships across a dataset of 468 fish species (254 marine, 191 freshwater, and 23 that occupy both habitats) in relation to body mass and fish length. Herbivores had significantly relatively stouter bodies and longer intestines than omni- and faunivores. Among faunivores, corallivores had longer intestines than invertivores, with piscivores having the shortest. There were no detectable differences between herbivore groups, possibly due to insufficient understanding of herbivorous fish diets. We propose that reasons for long intestines in fish include (i) difficult-to-digest items that require a symbiotic microbiome, and (ii) the dilution of easily digestible compounds with indigestible material (e.g., sand, wood, exoskeleton). Intestinal indices differed significantly between dietary groups, but there was substantial group overlap. Counter-intuitively, in the largest dataset, marine species had significantly shorter intestines than freshwater fish. These results put fish together with mammals as vertebrate taxa with clear convergence in intestine length in association with trophic level, in contrast to reptiles and birds, even if the peculiar feeding ecology of herbivorous fish is probably more varied than that of mammalian herbivores.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11160-024-09853-3.

Protective effect of San Huang Pill and its bioactive compounds against ulcerative colitis in Drosophila via modulation of JAK/STAT, apoptosis, Toll, and Nrf2/Keap1 pathways

ETHNOPHARMACOLOGICAL RELEVANCE

San Huang Pill (SHP) is a prescription in Dunhuang Ancient Medical Prescription, which has the efficacy of heat-clearing and dampness-drying, and is a traditional formula for the treatment of gastrointestinal diseases. However, its efficacy and mechanism in treating ulcerative colitis (UC) are still unclear.

AIM OF THE STUDY

To investigate the protective effects of SHP and its bioactive compounds against Dextran Sulfate Sodium (DSS)-induced intestinal damage using the Drosophila melanogaster model, and to detect the molecular mechanism of SHP in the treatment of UC.

METHODS

Survival rate, locomotion, feeding, and excretion were used to explore the anti-inflammatory effects of SHP. The pharmacotoxicity of SHP was measured using developmental analysis. Intestinal integrity, intestinal length, intestinal acid-base homeostasis, and Tepan blue assay were used to analyze the protective effect of SHP against DSS-induced intestinal damage. The molecular mechanism of SHP was detected using DHE staining, immunofluorescence, real-time PCR, 16 S rRNA gene sequencing, and network pharmacology analysis. Survival rate, intestinal length, and integrity analysis were used to detect the protective effect of bioactive compounds of SHP against intestinal damage.

RESULTS

SHP supplementation significantly increased the survival rate, restored locomotion, increased metabolic rate, maintained intestinal morphological integrity and intestinal homeostasis, protected intestinal epithelial cells, and alleviated intestinal oxidative damage in adult flies under DSS stimulation. Besides, administration of SHP had no toxic effect on flies. Moreover, SHP supplementation remarkably decreased the expression levels of genes related to JAK/STAT, apoptosis, and Toll signaling pathways, increased the gene expressions of the Nrf2/Keap1 pathway, and also reduced the relative abundance of harmful bacteria in DSS-treated flies. Additionally, the ingredients in SHP (palmatine, berberine, baicalein, wogonin, rhein, and aloeemodin) had protection against DSS-induced intestinal injury, such as prolonging survival rate, increasing intestinal length, and maintaining intestinal barrier integrity.

CONCLUSION

SHP had a strong anti-inflammatory function, and remarkably alleviated DSS-induced intestinal morphological damage and intestinal homeostatic imbalance in adult flies by regulating JAK/STAT, apoptosis, Toll and Nrf2/Keap1 signaling pathways, and also gut microbial homeostasis. This suggests that SHP may be a potential complementary and alternative medicine herb therapy for UC, which provides a basis for modern pharmacodynamic evaluation of other prescriptions in Dunhuang ancient medical prescription.

The physiological responses to titanium dioxide nanoparticles exposure in pearl oysters (Pinctada fucata martensii)

To evaluate the physiological responses to titanium dioxide nanoparticles exposure in pearl oysters (Pinctada fucata martensii), pearl oysters were exposed for 14 days to different levels (0.05, 0.5, and 5 mg/L) of nano-TiO2 suspensions, while a control group did not undergo any nano-TiO2 treatment. And then recovery experiments were performed for 7 days without nano-TiO2 exposure. At days 1, 3, 7, 14, 17, and 21, hepatopancreatic tissue samples were collected and used to examine the activities of protease, amylase, lipase, catalase (CAT), glutathione peroxidase (GPx), superoxide dismutase (SOD), lysozyme (LYS), alkaline phosphatase (AKP), and acid phosphatase (ACP). The microstructure of the nacreous layer in shell was also analyzed by scanning electron microscopy. Results showed that pearl oysters exposed to 5 mg/L of TiO2 nanoparticles had significantly lower protease, amylase, and lipase activities and significantly higher CAT, SOD, GPx, LYS, ACP, and AKP activities than control pearl oysters did even after 7-day recovery (P-values <0.05). Pearl oysters exposed to 0.5 mg/L or 0.05 mg/L of TiO2 nanoparticles had lower protease, amylase, and lipase activities and higher CAT, SOD, GPx, LYS, ACP, and AKP activities than control pearl oysters did during the exposure period. After 7-day recovery, no significant differences in protease, lipase, SOD, GPx, CAT, ACP, AKP, or LYS activities were observed between pearl oysters exposed to 0.05 mg/L of TiO2 nanoparticles and control pearl oysters (P-values >0.05). In the period from day 7 to day 14, indistinct and irregular nacreous layer crystal structure in shell was observed. This study demonstrates that TiO2 nanoparticles exposure influences the levels of digestion, immune function, oxidative stress, and biomineralization in pearl oysters, which can be partially and weakly alleviated by short-term recovery. These findings contribute to understanding the mechanisms of action of TiO2 nanoparticles in bivalves. However, studies should evaluate whether a longer recovery period can restore to their normal levels in the future.

Consistent seasonal flexibility of the gut and its regions across wild populations of a winter-quiescent fish

Seasonality in north-temperate environments imposes drastic temperature and resource variations that shape the seasonal ecophysiology of resident organisms. A better understanding of an organism's capacity to flexibly respond to this drastic seasonal variation may reveal important mechanisms for tolerating or responding to environmental variation introduced by global change. In fishes, the digestive system is both the interface between resource and energy acquisition and one of the most expensive organ systems to maintain. However, little evidence describing the capacity for seasonal flexibility in the digestive tract of wild northern fishes exists. Here, we investigated phenotypic flexibility in the size of the gastrointestinal (GI) tract across three northern populations of a winter-dormant warm-water fish, pumpkinseed sunfish (Lepomis gibbosus). In all populations, pumpkinseed exhibited pronounced structural flexibility in the GI tract, aligned with winter and the timing of reproduction. The dry mass of the GI increased by 1.3- to nearly 2.5-fold in the early spring. The pyloric caeca demonstrated the greatest capacity for flexibility, increasing by up to 3.7-fold prior to reproduction. In all populations, minimum dry GI mass was consistently achieved during winter and mid-summer. This capacity for gut flexibility may represent a novel mechanism for facilitating rapid adaptive responses (e.g. metabolic plasticity) to future environmental change.

Dietary fatty acids and flight-training influence the expression of the eicosanoid hormone prostacyclin in songbirds

Diet shifts can alter tissue fatty acid composition in birds, which is subsequently related to metabolic patterns. Eicosanoids, short-lived fatty acid-derived hormones, have been proposed to mediate these relationships but neither baseline concentrations nor the responses to diet and exercise have been measured in songbirds. We quantified a stable derivative of the vasodilatory eicosanoid prostacyclin in the plasma of male European Starlings (Sturnus vulgaris, N = 25) fed semisynthetic diets with either high (PUFA) or low (MUFA) amounts of n6 fatty acid precursors to prostacyclin. Plasma samples were taken from each bird before, immediately after, and two days following a 15-day flight-training regimen that a subset of birds (N = 17) underwent. We found elevated prostacyclin levels in flight-trained birds fed the PUFA diet compared to those fed the MUFA diet and a positive relationship between prostacyclin and body condition, indexed by fat score. Prostacyclin concentrations also significantly decreased at the final time point. These results are consistent with the proposed influences of precursor availability (i.e., dietary fatty acids) and regulatory feedback associated with exercise (i.e., fuel supply and inflammation), and suggest that prostacyclin may be an important mediator of dietary influence on songbird physiology.

Rapid adaptation of the rainbow trout intestinal microbiota to the use of a high-starch 100% plant-based diet

Short-term adaptation of the microbiota could promote nutrient degradation and the host health. While numerous studies are currently undertaking feeding trials using sustainable diets for the aquaculture industry, the extent to which the microbiota adapts to these novel diets is poorly described. The incorporation of carbohydrates (CHO) within a 100% plant-based diet could offer a novel, cost-effective energy source that is readily available, potentially replacing the protein component in the diets. In this study, we investigated the short-term (3 weeks) effects of a high CHO, 100% plant-based diet on the mucosal and digesta associated microbiota diversity and composition, as well as several metabolic parameters in rainbow trout. We highlighted that the mucosa is dominated by Mycoplasma (44.86%). While the diets did not have significant effects on the main phyla (Proteobacteria, Firmicutes, and Actinobacteria), after 3 weeks, a lower abundance of Bacillus genus, and higher abundances of four lactic-acid bacteria were demonstrated in digesta. In addition, no post-prandial hyperglycemia was observed with high carbohydrate intake. These results provide evidence for the rapid adaptation of the gut microbiota and host metabolism to high CHO in combination with 100% plant ingredients in rainbow trout.

Differential modulation of digestive enzymes and energy reserves at different times after feeding in juveniles of the marine estuarine-dependent flatfish Paralichthys orbignyanus (Valenciennes, 1839)

Integrative studies are lacking on the responses of digestive enzymes and energy reserves in conjunction with morphological traits at distinct postprandial times in marine estuarine-dependent flatfishes of ecological and economic importance, such as Paralichthys orbignyanus. We determined total weight (TW), hepato-somatic index (IH), activities of digestive enzymes in the intestine, and the concentration of energy reserves in the liver and the muscle at 0, 24, 72, and 360 h after feeding in juveniles of P. orbignyanus. Amylase activity decreased at 72 h (about 30%). Maltase, sucrose, and lipase activities reached peak at 24 h (67%, 600%, and 35%, respectively). Trypsin and aminopeptidase-N activities at 24 and 72 h, respectively, were lower than those at t = 0 (53% and 30%). A peak increase in the concentration of glycogen and triglycerides in the liver (24 h) (86% and 89%, respectively) occurred. In muscle, glycogen and triglyceride concentrations were unchanged at 24 h and higher at 72 and 360 h (100% and 60%). No changes were found in TW, IH, free glucose in the liver and muscle, and protein in the liver. The protein concentration in the muscle sharply increased at 24 and 360 h after feeding (60%). The results indicate a distinct and specific response of central components of carbohydrate, lipid, and protein metabolism that could be adjustments at the biochemical level upon periods of irregular feeding and even of long-term food deprivation inside coastal lagoons or estuaries. The distinct responses of digestive enzymes in the intestine and energy reserves in the liver and muscle suggest the differential modulation of tissue-specific anabolic and catabolic pathways that would allow the maintenance of physical conditions.

Teeth and the gastrointestinal tract in mammals: when 1 + 1 = 3

Both teeth and the digestive tract show adaptations that are commonly interpreted in the context of trophic guilds-faunivory, herbivory and omnivory. Teeth prepare food for the digestive tract, and dental evolution focuses on increasing durability and functionality; in particular, size reduction of plant particles is an important preparation for microbial fermentative digestion. In narratives of digestive adaptations, microbes are typically considered as service providers, facilitating digestion. That the majority of 'herbivorous' (and possibly 'omnivorous') mammals display adaptations to maximize microbes' use as prey-by harvesting the microbes multiplying in their guts-is less emphasized and not reflected in trophic labels. Harvesting of microbes occurs either via coprophagy after separation from indigestible material by a separation mechanism in the hindgut, or from a forestomach by a 'washing mechanism' that selectively removes fines, including microbes, to the lower digestive tract. The evolution of this washing mechanism as part of the microbe farming niche opened the opportunity for the evolution of another mechanism that links teeth and guts in an innovative way-the sorting and cleaning of not-yet-sufficiently-size-reduced food that is then re-submitted to repeated mastication (rumination), leading to unprecedented chewing and digestive efficiency. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

Convergence of gut microbiota in myrmecophagous amphibians

The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.

Rapid genome functional annotation pipeline anchored to the house sparrow (Passer domesticus, Linnaeus 1758) genome reannotation

The house sparrow (Passer domesticus) is a valuable avian model for studying evolutionary genetics, development, neurobiology, physiology, behavior, and ecology, both in laboratory and field-based settings. The current annotation of the P. domesticus genome available at the Ensembl Rapid Release site is primarily focused on gene set building and lacks functional information. In this study, we present the first comprehensive functional reannotation of the P. domesticus genome using intestinal Illumina RNA sequencing (RNA-Seq) libraries. Our revised annotation provides an expanded view of the genome, encompassing 38592 transcripts compared to the current 23574 transcripts in Ensembl. We also predicted 14717 protein-coding genes, achieving 96.4% completeness for Passeriformes lineage BUSCOs. A substantial improvement in this reannotation is the accurate delineation of untranslated region (UTR) sequences. We identified 82.7% and 93.8% of the transcripts containing 5'- and 3'-UTRs, respectively. These UTR annotations are crucial for understanding post-transcriptional regulatory processes. Our findings underscore the advantages of incorporating additional specific RNA-Seq data into genome annotation, particularly when leveraging fast and efficient data processing capabilities. This functional reannotation enhances our understanding of the P. domesticus genome, providing valuable resources for future investigations in various research fields.

Seasonal flexibility of the gut structure and physiology in Eremias multiocellata

Although gut seasonal plasticity has been extensively reported, studies on physiological flexibility, such as water-salt transportation and motility in reptiles, are limited. Therefore, this study investigated the intestinal histology and gene expression involved in water-salt transport (AQP1, AQP3, NCC, and NKCC2) and motility regulation (nNOS, CHRM2, and ADRB2) in desert-dwelling Eremias multiocellata during winter (hibernating period) and summer (active period). The results showed that mucosal thickness, the villus width and height, the enterocyte height of the small intestine, and the mucosal and submucosal thicknesses of the large intestine were greater in winter than in summer. However, submucosal thickness of the small intestine and muscularis thickness of the large intestine were lower in winter than in summer. Furthermore, AQP1, AQP3, NCC, nNOS, CHRM2, and ADRB2 expressions in the small intestine were higher in winter than in summer; AQP1, AQP3, and nNOS expressions in the large intestine were lower in winter than in summer, with the upregulation of NCC and CHRM2 expressions; no significant seasonal differences were found in intestinal NKCC2 expression. These results suggest that (i) intestinal water-salt transport activity is flexible during seasonal changes where AQP1, AQP3 and NCC play a vital role, (ii) the intestinal motilities are attenuated through the concerted regulation of nNOS, CHRM2, and ADRB2, and (iii) the physiological flexibility of the small and large intestine may be discrepant due to their functional differences. This study reveals the intestinal regulation and adaptation mechanisms in E. multiocellata in response to the hibernation season.

Effects of Honeysuckle Varieties on Protective and Detoxifying Enzyme Activities in Heterolocha Jinyinhuaphaga Chu (Lepidoptera: Geometridae) Larvae

Investigating the effects of various host plants on protective and detoxifying enzyme activities in insects could provide insights into the adaptation mechanisms of insects to host plants. In the present study, we measured superoxide dismutase (SOD), peroxidase (POD), catalase(CAT), carboxylesterase(CarE), acetylcholinesterase (AchE), and glutathione S-transferase (GST) activity levels in Heterolocha jinyinhuaphaga Chu (Lepidoptera: Geometridae) larvae fed on four honeysuckle varieties (wild variety, Jiufeng 1, Xiangshui 1, and Xiangshui 2). The results showed that levels of SOD, POD, CAT, CarE, AchE, and GST activities in H. jinyinhuaphaga larvae fed on the four honeysuckle varieties differed. The enzyme activity levels were the highest when larvae were fed on the wild variety, followed by Jiufeng 1 and Xiangshui 2, and the lowest when fed on Xiangshui 1. Furthermore, the enzyme activity levels increased with an increase in larval age. According to the results of two - way analysis of variance, the interaction between host plants and larval age had no significant effect on SOD, POD, CAT, CarE, AchE, and GST activities in H. jinyinhuaphaga larvae (p ˃0.05).

Reptilian digestive efficiency: Past, present, and future

Digestion and assimilation of nutrients and energy is central to survival. At its most basic level, investigations of digestion in animals must examine digestive efficiency, or how much of a given meal (i.e., energy) or a specific nutrient an organism can acquire from its food. There are many studies examining this in reptiles, but there is large variation in methodology, and thus, in the conclusions drawn from the gathered data. The majority rely on ratio-based analyses that can jeopardize the reliability of their findings. Therefore, we reviewed the literature to identify common themes in the digestive efficiency data on reptiles. Due to the sheer number of available studies, we largely focused on lizards, but included data on all reptilian groups. As an example of what the current data can reveal, we performed a meta-analysis of digestive efficiency in lizards as a function of temperature using regression analyses. We detected a weak positive trend of soluble carbohydrate digestibility as a function of temperature, but no similar trend in broad-scale digestive efficiency, and propose that these patterns be reevaluated with non-ratio data. We conclude with calls to end conducting analyses on ratios and instead employ covariate methods, for more studies of reptilian digestive efficiency and related processes using consistent methodology, more representation of each population (e.g., many studies focus on males only), and more detailed studies examining the effects of temperature on digestion (since the current data are inconclusive).

Effect of allelochemicals sustained-release microspheres on the ingestion, incorporation, and digestion abilities of Daphnia magna Straus

Allelochemicals sustained-release microspheres (ACs-SMs) exhibited great inhibition effect on algae, however, few studies have focused on ACs-SMs toxicity on invertebrate. In this study, the effects of single high-concentration ACs (15 mg/L, SH-ACs), repeated low-concentration ACs (3 × 5 mg/L, RL-ACs) and ACs-SMs containing 15 mg/L ACs exposure on the ingestion, incorporation, and digestion of Daphnia magna Straus (DS) were investigated by stable isotope ¹⁵N labeling method. Meanwhile, the diversity and abundance of microflora in DS guts were determined by 16S rRNA genes and cloning methods. The results showed that SH-ACs exposure caused 50% and 33.3% death rates for newborn and adult DS, while RL-ACs exposure caused 10% death rate for newborn DS and no obvious effect on the activity of adult DS. And ACs-SMs exposure did not diminish the motility of both newborn and adult DS, indicating the lower acute toxicity of ACs-SMs. Furthermore, SH-ACs inhibited the ingestion (-6.45%), incorporation (-47.1%) and digestion (-53.8%) abilities of DS and reduced the microbial abundance (-27.7%) in DS guts. Compared with SH-ACs, RL-ACs showed relatively low impact on the ingestion (-3.23%), incorporation (-5.89%) and digestion (-23.9%) abilities of DS. Interestingly, ACs-SMs enhanced the ingestion (+9.68%), incorporation (+52.9%) and digestion (+51.3%) abilities of DS and increased the microbial abundance (+10.7%) in DS guts. Overall ACs and ACs-SMs reduced the diversity of microflora in DS guts. In conclusion, ACs-SMs can release ACs sustainably and prolong the sustained release time, which not only effectively reduce the toxicity of ACs, but also had positive effects on DS.

Effect of gluten on the digestive tract and fat body of Telodeinopus aoutii (Diplopoda)

Adult specimens or larvae of invertebrates used as food for vertebrates are often maintained close to gluten so they might become vectors for cereal proteins. However, the tissues and internal organs can respond differently in animals with different feeding habits. The midgut epithelium might be a first and sufficient barrier preventing uptake and effects of gluten on the whole body, while the fat body is the main organ that accumulates different xenobiotics. Good models for such research are animals that do not feed on gluten-rich products in their natural environment. The project's goal was to investigate alterations in the midgut epithelium and fat body of the herbivorous millipede Telodeinopus aoutii (Diplopoda) and analyze cell death processes activated by gluten. It enabled us to determine whether changes were intensified or reversed by adaptive mechanisms. Adult specimens were divided into control and experimental animals fed with mushrooms supplemented with gluten and analyzed using transmission electron microscopy, flow cytometry, and confocal microscopy. Two organs were isolated for the qualitative and quantitative analysis: the midgut and the fat body. Our study of the herbivorous T. aoutii which does not naturally feed on gluten containing diet showed that continuous and prolonged gluten feeding activates repair processes that inhibit the processes of cell death (apoptosis and necrosis) and induce an increase in cell viability.

Lactation from the inside out: Maternal homeorhetic gastrointestinal adaptations regulating energy and nutrient flow into milk production

Lactation invokes homeorhetic processes to ramp up and supply milk synthesis components to fulfil nutritional, immunological and microbiological requirements of developing offspring, overseen by complex neuroendocrine networks. The maternal gut meets these intense metabolic demands, supported by hyperphagia and rapid adjustments to process larger food quantities. Enteroplasticity describes an inherent ability of the gastrointestinal tract to harness metabolic and structural adaptations that increase nutrient absorption. Most shifts in response to increased demands are transitory and by secreting milk, the continuous energetic drain out of the maternal body avoids development of pathological metabolic diseases. Lactation has various positive benefits for long-term maternal health but many females do not lactate for long post pregnancy and younger women are increasingly pre-disposed to excessive body mass and/or metabolic complications prior to reproducing. Inadvertently invoking intestinal adaptations to harvest and store excess nutrients has negative health implications with increased risks for both mother and offspring.

Multi-omics provide mechanistic insight into the Pb-induced changes in tadpole fitness-related traits and environmental water quality

Water pollution from lead/Pb²⁺ poses a significant threat to aquatic ecosystems, and its repercussions on aquatic animals have received considerable attention. Although Pb²⁺ has been found to affect numerous aspects of animals, including individual fitness, metabolic status, and symbiotic microbiota, few studies have focused on the associations between Pb²⁺-induced variations in fitness, metabolome, symbiotic microbiome, and environmental parameters in the same system, limiting a comprehensive understanding of ecotoxicological mechanisms from a holistic perspective. Moreover, most ecotoxicological studies neglected the potential contributions of anions to the consequences generated by inorganic lead compounds. We investigated the effects of Pb(NO₃)₂ at environmentally relevant concentrations on the Rana omeimontis tadpoles and the water quality around them, using blank and NaNO₃-treated groups as control. Results showed that Pb(NO₃)₂ not only induced a rise in water nitrite level, but exposure to this chemical also impaired tadpole fitness-related traits (e.g., growth and development). The impacts on tadpoles were most likely a combination of Pb²⁺ and NO₃^-. Tissue metabolomics revealed that Pb(NO₃)₂ exposure influenced animal substrate (i.e., carbohydrate, lipid, and amino acid) and prostaglandin metabolism. Pb(NO₃)₂ produced profound shifts in gut microbiota, with increased Proteobacteria impairing Firmicutes, resulting in higher aerobic and possibly pathogenic bacteria. NaNO₃ also influenced tadpole metabolome and gut microbiome, in a manner different to that of Pb(NO₃)₂. The presence of NO₃^- seemed to counteract some changes caused by Pb²⁺, particularly on the microbiota. Piecewise structural equation model and correlation analyses demonstrated connections between tissue metabolome and gut microbiome, and the variations in tadpole phenotypic traits and water quality were linked to changes in tissue metabolome and gut microbiome. These findings emphasized the important roles of gut microbiome in mediating the effects of toxin on aquatic ecosystem. Moreover, it is suggested to consider the influences of anions in the risk assessment of heavy metal pollutions.

Diet evolution of carnivorous and herbivorous mammals in Laurasiatheria

Background

Laurasiatheria contains taxa with diverse diets, while the molecular basis and evolutionary history underlying their dietary diversification are less clear.

Results

In this study, we used the recently developed molecular phyloecological approach to examine the adaptive evolution of digestive system-related genes across both carnivorous and herbivorous mammals within Laurasiatheria. Our results show an intensified selection of fat and/or protein utilization across all examined carnivorous lineages, which is consistent with their high-protein and high-fat diets. Intriguingly, for herbivorous lineages (ungulates), which have a high-carbohydrate diet, they show a similar selection pattern as that of carnivorous lineages. Our results suggest that for the ungulates, which have a specialized digestive system, the selection intensity of their digestive system-related genes does not necessarily reflect loads of the nutrient components in their diets but appears to be positively related to the loads of the nutrient components that are capable of being directly utilized by the herbivores themselves. Based on these findings, we reconstructed the dietary evolution within Laurasiatheria, and our results reveal the dominant carnivory during the early diversification of Laurasiatheria. In particular, our results suggest that the ancestral bats and the common ancestor of ruminants and cetaceans may be carnivorous as well. We also found evidence of the convergent evolution of one fat utilization-related gene, APOB, across carnivorous taxa.

Conclusions

Our molecular phyloecological results suggest that digestive system-related genes can be used to determine the molecular basis of diet differentiations and to reconstruct ancestral diets.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02033-6.

The cloacal microbiome of a cavity-nesting raptor, the lesser kestrel (Falco naumanni)

Background

Microbial communities are found on any part of animal bodies exposed to the environment, and are particularly prominent in the gut, where they play such a major role in the host metabolism and physiology to be considered a "second genome". These communities, collectively known as "microbiome", are well studied in humans and model species, while studies on wild animals have lagged behind. This is unfortunate, as different studies suggested the central role of the gut microbiome in shaping the evolutionary trajectories of species and their population dynamics. Among bird species, only few descriptions of raptor gut microbiomes are available, and mainly carried out on captive individuals.

Objectives

In this study, we aimed at improving the knowledge of raptor microbiomes by providing the first description of the gut microbiome of the lesser kestrel (Falco naumanni), a cavity-nesting raptor.

Results

The gut microbiome of the lesser kestrel was dominated by Actinobacteria (83.9%), Proteobacteria (8.6%) and Firmicutes (4.3%). We detected no differences in microbiome composition between males and females. Furthermore, the general composition of the microbiome appears similar to that of phylogenetically distant cavity-nesting species.

Conclusions

Our results broaden the knowledge of raptor gut microbial communities and let us hypothesize that the distinct nest environment in terms of microclimate and presence of organic material from previous breeding attempts, to which cavity-nesting species that reuse the nest are exposed, might be an important driver shaping microbiomes.

Ambush predation and the origin of euprimates

Primates of modern aspect (euprimates) are characterized by a suite of characteristics (e.g., convergent orbits, grasping hands and feet, reduced claws, and leaping), but the selective pressures responsible for the evolution of these euprimate characteristics have long remained controversial. Here, we used a molecular phyloecological approach to determine the diet of the common ancestor of living primates (CALP), and the results showed that the CALP had increased carnivory. Given the carnivory of the CALP, along with the general observation that orbital convergence is largely restricted to ambush predators, our study suggests that the euprimate characteristics could have been more specifically adapted for ambush predation. In particular, our behavior experiment further shows that nonclaw climbing can significantly reduce noises, which could benefit the ancestral euprimates' stalking to ambush their prey in trees. Therefore, our study suggests that the distinctive euprimate characteristics may have evolved as their specialized adaptation for ambush predation in arboreal environments.

The Complex and Well-Developed Morphological and Histological Structures of the Gastrointestinal Tract of the Plateau Zokor Improve Its Digestive Adaptability to High-Fiber Foods

The morphological and histological traits of the gastrointestinal tract (GIT) enable the animal to perform some specific functions that enhance the species’ adaptability to environments. The plateau zokor (Eospalax baileyi) is a subterranean rodent that mainly forages on plant roots in the Qinghai-Tibet Plateau, but little is known about the mechanism by which the plateau zokor digests roots that have high fiber contents. In this study, we used comparative anatomy methods to compare the morphological and histological traits of the GIT of both the plateau zokor and the plateau pika (Ochotona curzoniae), a small, fossorial lagomorph that forages aboveground plant parts, in order to clarify the traits of the plateau zokor’s GIT and to understand its adaptations to high-fiber foods. The results showed that the foods which plateau zokors eat have a higher fiber content than those which the plateau pikas eat. The plateau zokor has a double-chambered and hemi-glandular stomach (the tubular glands are only in the gastric corpus II, and the gastric fundus is keratinized), whereas the plateau pika has a simple, wholly glandular stomach. The gross morphological indicators (organ index and relative length) of the GIT were significantly lower in the plateau zokor than they were in the plateau pika (p < 0.001). However, the thickness of the gastric corpus II mucosal layer and the gastric fundus muscle layer are significantly higher in the plateau zokor than they are in the plateau pika (p < 0.001), and the thickness of each layer of intestinal tissue is higher in the plateau zokor than it is in the plateau pika. Additionally, the small intestinal villi also are higher and wider in the plateau zokor than they are in the plateau pika. Our results suggest that instead of adapting to digest the high-fiber diet by expanding the size of the GIT, the plateau zokor has evolved a complex stomach and a well-developed gastrointestinal histological structure, and that these specialized GIT structures are consistent with an optimal energy-economy evolutionary adaptation strategy.

Diet, habitat and flight characteristics correlate with intestine length in birds

A link between diet and avian intestinal anatomy is generally assumed. We collated the length of intestinal sections and body mass of 390 bird species and tested relationships with diet, climate and locomotion. There was a strong phylogenetic signal in all datasets. The total and small intestine scaled more-than-geometrically (95%CI of the scaling exponent > 0.33). The traditional dietary classification (faunivore, omnivore and herbivore) had no significant effect on total intestine (TI) length. Significant dietary proxies included %folivory, %frugi-nectarivory and categories (frugi-nectarivory, granivory, folivory, omnivory, insectivory and vertivory). Individual intestinal sections were affected by different dietary proxies. The best model indicates that higher consumption of fruit and nectar, drier habitats, and a high degree of flightedness are linked to shorter TI length. Notably, the length of the avian intestine depends on other biological factors as much as on diet. Given the weak dietary signal in our datasets, the diet intestinal length relationships lend themselves to narratives of flexibility (morphology is not destiny) rather than of distinct adaptations that facilitate using one character (intestine length) as proxy for another (diet). Birds have TIs of about 85% that of similar-sized mammals, corroborating systematic differences in intestinal macroanatomy between vertebrate clades.

Macronutrient signals for adaptive modulation of intestinal digestive enzymes in two omnivorous Galliformes

According to the adaptive modulation hypothesis, digestive enzyme activities are matched to their respective dietary substrate level so that ingested nutrients are not wasted in excreta due to insufficient digestive capacity, and so membrane space or expenditures building/maintaining the intestinal hydrolytic machinery are not wasted when substrate levels are low. We tested predictions in juvenile northern bobwhites (Colinus virginianus) and juvenile and adult domestic chickens (Gallus gallus domesticus) by feeding them on diets varying in starch, protein, and lipid composition for 7-9 d (bobwhites) or 15 d (chickens). Birds were euthanized, intestinal tissue harvested, and enzyme activities measured in tissue homogenates from proximal, medial and distal small intestine. We found that (1) α-glucosidase (AG; maltase and sucrase) activities were induced by dietary starch in both juvenile and adult chickens but not in northern bobwhites; (2) aminopeptidase-N (APN) activities were induced by dietary protein in both bobwhites and juvenile but not adult chickens; (3) AG activities were suppressed by an increase in dietary lipid in both bobwhites and juvenile but not adult chickens; and (4) APN activities were not suppressed by high dietary lipid in any birds. We review findings from 35 analogous trials in 16 avian species. 100% of avian omnivores modulate at least one enzyme in response to change in dietary substrate level. AG induction by dietary carbohydrate occurs in more members of Galloanserae than in Neoaves, and all omnivorous members of Neoaves tested so far increase APN activity on high dietary protein, whereas fewer of the Galloanserae do.

Prejuveniles of Mugil liza (Actinopterygii; Fam. Mugilidae) show digestive and metabolic flexibility upon different postprandial times and refeeding

Many animals face periods of feeding restrictions implying fasting and refeeding. The determination of digestive/metabolic and body condition parameters at different times of food deprivation and after refeeding allows to evaluate the postprandial dynamics, the transition from feeding to fasting and the capacity to reverse digestive and metabolic alterations. In spite of its physiological importance, studies on estuarine-dependent detritivore fish are lacking. We determined total mass (TM), relative intestine length (RIL), hepatosomatic index (HSI), digestive enzymes activities in the intestine and energy reserves in liver and muscle at 0, 24, 72, 144 and 240 h after feeding and at 72 h after refeeding in prejuveniles of Mugil liza (Mugilidae) as a model species. After feeding, a decrease occurred in: TM (144 h, 25%), RIL (144 h, 23%); amylase and maltase (72 h, 45 and 35%), sucrase (24 h, 40%) and lipase (24 h, 70%) in intestine; glycogen and free glucose (72 h, 90 and 92%) in liver. In muscle, glycogen (72-144 h) and free glucose (144 h) (170% and 165%, respectively) peak increased; triglycerides decreased at 24-240 h (50%). After refeeding TM, RIL, carbohydrases activities in intestine, glycogen and free glucose in liver were recovered. In muscle, glycogen and free glucose were similar to 0 h; lipase activity and triglycerides were not recovered. Trypsin and APN in intestine, triglycerides in liver, protein in liver and muscle and HSI did not change. The differential modulation of key components of carbohydrates and lipid metabolism after feeding/refeeding would allow to face fasting and recover body condition. Our results improve lacking knowledge about digestive and metabolic physiology of detritivore fish.

Prevalence of mouthpart sensilla and protease producing symbiotic gut bacteria in the forensic fly Chrysomya megacephala (Fabricius, 1794): Insight from foraging to digestion

The blow fly, Chrysomya megacephala (Fabricius, 1794) is a globally prevalent forensically important species that helps to estimate accurate postmortem interval since the death. This fly occasionally causes cutaneous myiasis and transmits several pathogenic bacteria. To understand their ability of corpse detection and digestion of protein-rich meal, the present study describes the mouthpart sensilla and assessment of protease producing symbiotic gut bacteria. Scanning electron microscopy (SEM) showed the prevalence of trichoid sensilla (Tr), basiconic sensilla (Ba) and microtrichia (Mr) on labellar lobes, haustellum and maxillary palps of mouthparts. Bacterial particles of both rod (small and large) and spherical shaped were detected in the gut of C. megacephala using SEM. The bacterial density was higher on the foregut and midgut in comparison to the hindgut. From 72 bacterial isolates, 10 isolates from the foregut region showed considerable protease-producing efficacy ranging between 3.98 - 6.83 GHR and 9.73 - 34.68 U/ml protease. Among these, the most promising protease-producing bacterial isolate showed 16S rDNA sequence similarity (99.85%) with Chryseobacterium artocarpi DNA. This bacterium was the first report from flies. The findings of the study might help in better understanding of the role of sensilla in host perception and foregut symbiotic bacterial association in protein digestion in C. megacephala.

Gut Microbial Community and Host Thermoregulation in Small Mammals

The endotherms, particularly the small mammals living in the polar region and temperate zone, are faced with extreme challenges for maintaining stable core body temperatures in harsh cold winter. The non-hibernating small mammals increase metabolic rate including obligatory thermogenesis (basal/resting metabolic rate, BMR/RMR) and regulatory thermogenesis (mainly nonshivering thermogenesis, NST, in brown adipose tissue and skeletal muscle) to maintain thermal homeostasis in cold conditions. A substantial amount of evidence indicates that the symbiotic gut microbiota are sensitive to air temperature, and play an important function in cold-induced thermoregulation, via bacterial metabolites and byproducts such as short-chain fatty acids and secondary bile acids. Cold signal is sensed by specific thermosensitive transient receptor potential channels (thermo-TRPs), and then norepinephrine (NE) is released from sympathetic nervous system (SNS) and thyroid hormones also increase to induce NST. Meanwhile, these neurotransmitters and hormones can regulate the diversity and compositions of the gut microbiota. Therefore, cold-induced NST is controlled by both Thermo-TRPs—SNS—gut microbiota axis and thyroid—gut microbiota axis. Besides physiological thermoregulation, small mammals also rely on behavioral regulation, such as huddling and coprophagy, to maintain energy and thermal homeostasis, and the gut microbial community is involved in these processes. The present review summarized the recent progress in the gut microbiota and host physiological and behavioral thermoregulation in small mammals for better understanding the evolution and adaption of holobionts (host and symbiotic microorganism). The coevolution of host-microorganism symbionts promotes individual survival, population maintenance, and species coexistence in the ecosystems with complicated, variable environments.

Seasonal Variations in the Digestive Tract of the Little Owl, Athene noctua: Anatomical, Histological, and Scanning Electron Microscopical Studies

The digestive tract of the little owl, Athene noctua (Strigiformes: Strigidae), is described in two different seasons. The digestive tract of this bird follows the basic model for that of a predatory bird. The cervical esophagus is not expanded to form a crop. The internal surface of the esophagus forms numerous longitudinal folds provided with numerous mucous glands. These longitudinal folds increase in number and vary in depth posteriorly. The folds of the proventriculus are composed of simple branched tubular glands. The ventriculus is lined by a thin layer of koilin. The number of goblet cells gradually increases from the duodenum to the rectum, and the lymphatic tissue diffuses within the lamina propria. The esophageal glands secrete acid mucopolysaccharides, while the gastric glands of the stomach, the goblet cells, and crypts of Lieberkühn secrete acid mucopolysaccharides. Proteins were observed in the different histological structures of the digestive tract. Morphometric and histometric studies showed differences between summer and winter in the esophagus and glandular stomach (especially in winter), but no seasonal differences were seen in the muscular stomach, or small and large intestines.

Physiological effects of food availability times in higher vertebrates

Food availability is a crucial ecological determinant of population size and community structure, and controls various life-history traits in most, if not all, species. Food availability is not constant; there are daily and seasonal differences in food abundance. When coupled to appetite (urge to eat), this is expressed as the eating schedule of a species. Food availability times affect daily and seasonal physiology and behaviour of organisms both directly (by affecting metabolic homeostasis) and indirectly (by altering synchronization of endogenous rhythms). Restricted food availability times may, for example, constrain reproductive output by limiting the number or quality of offspring or the number of reproductive attempts, as has been observed for nesting frequency in birds. Consuming food at the wrong time of day reduces the reproductive ability of a seasonal breeder, and can result in quality-quantity trade-offs of offspring. The food availability pattern serves as a conditioning environment, and can shape the activity of the genome by influencing chromatin activation/silencing; however, the functional linkage of food availability times with epigenetic control of physiology is only beginning to emerge. This Review gives insights into how food availability times, affected by changes in eating schedules and/or by alterations in feeding environment or lifestyle, could have hitherto unknown consequences on the physiology and reproductive fitness of seasonally breeding vertebrates and those that reproduce year round.

Microbial Biogeography along the Gastrointestinal Tract Segments of Sympatric Subterranean Rodents (Eospalax baileyi and Eospalax cansus)

Simple Summary

The gut microbiota are crucial for hosts. For mammals, different gastrointestinal tract (GIT) segments have specific microbial communities, which play an essential role in the host’s nutrition, metabolism, immunity, and health. Plateau zokors (Eospalax baileyi) and Gansu zokors (Eospalax cansus) are closely related species that belong to the Spalacidae family, and are common pests in agriculture, forestry, and animal husbandry in northwestern China, with a sympatric distribution area in the transition zone between the Qinghai-Tibetan Plateau and the Loess Plateau. Here, the characteristics of the microbiota communities in different GIT segments of the plateau zokor and the Gansu zokor were studied, and the microbiota communities of the two zokor species were compared. Our results provide important information for further study on the function of microbiota communities in different GIT segments and the potential use of the gut microbiota as a new method for the population management of the zokors.

Abstract

In this study, based on high-throughput sequencing technology, the biodiversity and the community structure of microbiota in different GIT segments (the stomach, small intestine, cecum and rectum) of plateau zokors and Gansu zokors were studied and compared. A source tracking analysis for the microbial communities of different GIT segments was carried out using the fast expectation–maximization microbial source tracking (FEAST) method. We found that, for both species, the microbial community richness and diversity of the small intestine were almost the lowest while those of the cecum were the highest among the four segments of the GIT. Beta diversity analyses revealed that the bacterial community structures of different GIT segments were significantly different. As for the comparison between species, the bacterial community compositions of the whole GIT, as well as for each segment, were all significantly different. Source tracking conducted on both zokors indicated that the soil has little effect on the bacterial community of the GIT. A fairly high percentage of rectum source for the bacterial community of the stomach indicated that both zokors may engage in coprophagy.

The role of the gut microbiota in the dietary niche expansion of fishing bats

Background

Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet.

Results

We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish.

Conclusions

Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00137-w.

NMN Maintains Intestinal Homeostasis by Regulating the Gut Microbiota

The aim of this study was to determine the effects of long-term Nicotinamide mononucleotide (NMN) treatment on modulating gut microbiota diversity and composition, as well as its association with intestinal barrier function. In this study, C57BL/6J mice were fed different concentrations of NMN, and their feces were collected for detection of 16S rDNA and non-targeted metabolites to explore the effects of NMN on intestinal microbiota and metabolites. The results revealed that NMN increased the abundance of butyric acid-producing bacteria (Ruminococcae_UCG-014 and Prevotellaceae_NK3B31_group) and other probiotics (Akkermansia muciniphila), while the abundance of several harmful bacteria (Bilophila and Oscillibacter) were decreased after NMN treatment. Meanwhile, the level of bile acid-related metabolites in feces from the G1 group (0.1 mg/ml) was significantly increased compared to the control group, including cholic acid, taurodeoxycholic acid, taurocholic acid, glycocholic acid, and tauro-β-muricholic acid. In addition, long-term NMN treatment affected the permeability of the intestinal mucosa. The number of goblet cells and mucus thickness increased, as well as expression of tight junction protein. These results demonstrate that NMN reduced intestinal mucosal permeability and exerts a protective effect on the intestinal tract. This study lays the foundation for exploring NMN's utility in clinical research.

Larval nutrition impacts survival to adulthood, body size and the allometric scaling of metabolic rate in adult honeybees

Resting metabolic rate (RMR) is a fundamental physiological measure linked to numerous aspects of organismal function, including lifespan. Although dietary restriction in insects during larval growth/development affects adult RMR, the impact of the nutritional composition of larval diets (i.e. diet quality) on adult RMR has not been studied. Using in vitro rearing to control larval diet quality, we determined the effect of dietary protein and carbohydrate on honeybee survival to adulthood, time to eclosion, body mass/size and adult RMR. High carbohydrate larval diets increased survival to adulthood and time to eclosion compared with both low carbohydrate and high protein diets. Upon emergence, bees reared on the high protein diet were smaller and lighter than those reared on other diets, whilst those raised on the high carbohydrate diet varied more in body mass. Newly emerged adult bees reared on the high carbohydrate diet showed a significantly steeper increase in allometric scaling of RMR compared with those reared on other diets. This suggests that the nutritional composition of larval diets influences survival to adulthood, time to eclosion and the allometric scaling of RMR. Given that agricultural intensification and increasing urbanisation have led to a decrease in both forage availability and dietary diversity for bees, our results are critical to improving understanding of the impacts of poor developmental nutrition on bee growth/development and physiology.

Less need for differentiation? Intestinal length of reptiles as compared to mammals

Although relationships between intestinal morphology between trophic groups in reptiles are widely assumed and represent a cornerstone of ecomorphological narratives, few comparative approaches actually tested this hypothesis on a larger scale. We collected data on lengths of intestinal sections of 205 reptile species for which either body mass (BM), snout-vent-length (SVL) or carapax length (CL) was recorded, transforming SVL or CL into BM if the latter was not given, and analyzed scaling patterns with BM and SVL, accounting for phylogeny, comparing three trophic guilds (faunivores, omnivores, herbivores), and comparing with a mammal dataset. Length-BM relationships in reptiles were stronger for the small than the large intestine, suggesting that for the latter, additional factors might be relevant. Adding trophic level did not consistently improve model fit; only when controlling for phylogeny, models indicated a longer large intestine in herbivores, due to a corresponding pattern in lizards. Trophic level effects were highly susceptible to sample sizes, and not considered strong. Models that linked BM to intestine length had better support than models using SVL, due to the deviating body shape of snakes. At comparable BM, reptiles had shorter intestines than mammals. While the latter finding corresponds to findings of lower tissue masses for the digestive tract and other organs in reptiles as well as our understanding of differences in energetic requirements between the classes, they raise the hitherto unanswered question what it is that reptiles of similar BM have more than mammals. A lesser effect of trophic level on intestine lengths in reptiles compared to mammals may stem from lesser selective pressures on differentiation between trophic guilds, related to the generally lower food intake and different movement patterns of reptiles, which may not similarly escalate evolutionary arms races tuned to optimal agility as between mammalian predators and prey.

Historical contingency, geography and anthropogenic patterns of exposure drive the evolution of host switching in the Blastocystis species-complex

Parasites have the power to impose significant regulatory pressures on host populations, making evolutionary patterns of host switching by parasites salient to a range of contemporary ecological issues. However, relatively little is known about the colonization of new hosts by parasitic, commensal and mutualistic eukaryotes of metazoans. As ubiquitous symbionts of coelomate animals, Blastocystis spp. represent excellent candidate organisms for the study of evolutionary patterns of host switching by protists. Here, we apply a big-data phylogenetic approach using archival sequence data to assess the relative roles of several host-associated traits in shaping the evolutionary history of the Blastocystis species-complex within an ecological framework. Patterns of host usage were principally determined by geographic location and shared environments of hosts, suggesting that weight of exposure (i.e. propagule pressure) represents the primary force for colonization of new hosts within the Blastocystis species-complex. While Blastocystis lineages showed a propensity to recolonize the same host taxa, these taxa were often evolutionarily unrelated, suggesting that historical contingency and retention of previous adaptions by the parasite were more important to host switching than host phylogeny. Ultimately, our findings highlight the ability of ecological theory (i.e. ‘ecological fitting’) to explain host switching and host specificity within the Blastocystis species-complex.

Microbial colonization of the gastrointestinal tract of dairy calves - a review of its importance and relationship to health and performance

This review aims to explain how microbial colonization of the gastrointestinal tract (GIT) in young dairy calves is related to health and, consequently, to the performance of these animals. The review addresses everything from the fundamental aspects of microbial colonization to the current understanding about the microbiota manipulation to improve performance in adult animals. The ruminal microbiota is the most studied, mainly due to the high interest in the fermentative aspects, the production of short-chain fatty acids, and microbial proteins, and its effects on animal production. However, in recent years, the intestinal microbiota has gained space between studies, mainly due to the relationship to the host health and how it affects performance. Understanding how the GIT's microbiota looks like and how it is colonized may allow future studies to predict the best timing for dietary interventions as a way to manipulate it and, consequently, improve the health and performance of young ruminants.

Macro- and microstructures of the digestive tract in the Eurasian collared dove, Streptopelia decaocto (Frivaldszky 1838): Adaptive interplay between structure and dietary niche

We describe the functional morphology of the digestive tract of the Eurasian collared dove, Streptopelia decaocto using anatomical, morphometric, histological, histochemical, and ultrastructure techniques, and relate our findings to the species' dietary niche. Our results revealed that the esophagus is displaced on both sides of the neck and has highly folded tunica mucosa, which confer greater elasticity for efficient swallowing and passage of food to the crop. The proventriculus is delicate and its mucosal layer contains polymorphic glands with dense profound and superficial secretory units that open to the luminal surface by gastric pores. The ventriculus is biconvex and lined with a keratinized koilin membrane. The tubular glands within the mucosal lining include the isthmus, the neck, and the basal segment that comprise chief and basal cells with prominent nuclei. At the cuticle-mucosal interface, pyramidal vertical rodlets of the cuticle are secreted and superficially covered by a thin film of a horizontal matrix. The mucosa of the ileum form pyramidal villi that are oriented perpendicularly to the central lumen. Enterocytes infiltrated with goblet cells make up the epithelial lining of the villi. There are subtle differences in the thicknesses of corresponding tunics together with histochemical reactions of alcian blue (AB) and Masson-Goldner trichrome (MT) for their microstructures. Overall, our findings reveal remarkable convergence of both macro-and microstructures in S. decaocto to other granivorous species, and offer further evidence of the close association between functional morphology and feeding style relative to food swallowing, digestion, and absorption.

Molecular phyloecology suggests a trophic shift concurrent with the evolution of the first birds

Birds are characterized by evolutionary specializations of both locomotion (e.g., flapping flight) and digestive system (toothless, crop, and gizzard), while the potential selection pressures responsible for these evolutionary specializations remain unclear. Here we used a recently developed molecular phyloecological method to reconstruct the diets of the ancestral archosaur and of the common ancestor of living birds (CALB). Our results suggest a trophic shift from carnivory to herbivory (fruit, seed, and/or nut eater) at the archosaur-to-bird transition. The evolutionary shift of the CALB to herbivory may have essentially made them become a low-level consumer and, consequently, subject to relatively high predation risk from potential predators such as gliding non-avian maniraptorans, from which birds descended. Under the relatively high predation pressure, ancestral birds with gliding capability may have then evolved not only flapping flight as a possible anti-predator strategy against gliding predatory non-avian maniraptorans but also the specialized digestive system as an evolutionary tradeoff of maximizing foraging efficiency and minimizing predation risk. Our results suggest that the powered flight and specialized digestive system of birds may have evolved as a result of their tropic shift-associated predation pressure.

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

Duplications and Functional Convergence of Intestinal Carbohydrate-Digesting Enzymes

Vertebrate diets and digestive physiologies vary tremendously. Although the contribution of ecological and behavioral features to such diversity is well documented, the roles and identities of individual intestinal enzymes shaping digestive traits remain largely unexplored. Here, we show that the sucrase-isomaltase (SI)/maltase-glucoamylase (MGAM) dual enzyme system long assumed to be the conserved disaccharide and starch digestion framework in all vertebrates is absent in many lineages. Our analyses indicate that independent duplications of an ancestral SI gave rise to the mammalian-specific MGAM, as well as to other duplicates in fish and birds. Strikingly, the duplicated avian enzyme exhibits similar activities to MGAM, revealing an unexpected case of functional convergence. Our results highlight digestive enzyme variation as a key uncharacterized component of dietary diversity in vertebrates.

γδ T cells regulate the intestinal response to nutrient sensing

The intestine is a site of direct encounter with the external environment and must consequently balance barrier defense with nutrient uptake. To investigate how nutrient uptake is regulated in the small intestine, we tested the effect of diets with different macronutrient compositions on epithelial gene expression. We found that enzymes and transporters required for carbohydrate digestion and absorption were regulated by carbohydrate availability. The "on-demand" induction of this machinery required γδ T cells, which regulated this program through the suppression of interleukin-22 production by type 3 innate lymphoid cells. Nutrient availability altered the tissue localization and transcriptome of γδ T cells. Additionally, transcriptional responses to diet involved cellular remodeling of the epithelial compartment. Thus, this work identifies a role for γδ T cells in nutrient sensing.