Characterization of the gastrointestinal microbiome of the Syrian hamster (Mesocricetus auratus) and comparison to data from mice

Syrian hamsters (Mesocricetus auratus) have been increasingly used as rodent models in recent years, especially for SARS-CoV-2 since the pandemic. However, the physiology of this animal model is not yet well-understood, even less when considering the digestive tract. Generally, the gastrointestinal microbiome influences the immune system, drug metabolism, and vaccination efficacy. However, a detailed understanding of the gastrointestinal microbiome of hamsters is missing. Therefore, we analyzed 10 healthy 11-week-old RjHan:AURA hamsters fed a pelleted standard diet. Their gastrointestinal content was sampled (i.e., forestomach, glandular stomach, ileum, cecum, and colon) and analyzed using 16S rRNA gene amplicon sequencing. Results displayed a distinct difference in the bacterial community before and after the cecum, possibly due to the available nutrients and digestive functions. Next, we compared hamsters with the literature data of young-adult C57BL/6J mice, another important animal model. We sampled the same gastrointestinal regions and analyzed the differences in the microbiome between both rodents. Surprisingly, we found strong differences in their specific gastrointestinal bacterial communities. For instance, Lactobacillaceae were more abundant in hamsters' forestomach and ileum, while Muribaculaceae dominated in the mouse forestomach and ileum. Similarly, in mouse cecum and colon, Muribaculaceae were dominant, while in hamsters, Lachnospiraceae and Erysipelotrichaceae dominated the bacterial community. Molecular strains of Muribaculaceae in both rodent species displayed some species specificity. This comparison allows a better understanding of the suitability of the Syrian hamster as an animal model, especially regarding its comparability to other rodent models. Thereby, this work contributes to the characterization of the hamster model and allows better experimental planning.

Integrating microbiome science and evolutionary medicine into animal health and conservation

Microbiome science has provided groundbreaking insights into human and animal health. Similarly, evolutionary medicine - the incorporation of eco-evolutionary concepts into primarily human medical theory and practice - is increasingly recognised for its novel perspectives on modern diseases. Studies of host-microbe relationships have been expanded beyond humans to include a wide range of animal taxa, adding new facets to our understanding of animal ecology, evolution, behaviour, and health. In this review, we propose that a broader application of evolutionary medicine, combined with microbiome science, can provide valuable and innovative perspectives on animal care and conservation. First, we draw on classic ecological principles, such as alternative stable states, to propose an eco-evolutionary framework for understanding variation in animal microbiomes and their role in animal health and wellbeing. With a focus on mammalian gut microbiomes, we apply this framework to populations of animals under human care, with particular relevance to the many animal species that suffer diseases linked to gut microbial dysfunction (e.g. gut distress and infection, autoimmune disorders, obesity). We discuss diet and microbial landscapes (i.e. the microbes in the animal's external environment), as two factors that are (i) proposed to represent evolutionary mismatches for captive animals, (ii) linked to gut microbiome structure and function, and (iii) potentially best understood from an evolutionary medicine perspective. Keeping within our evolutionary framework, we highlight the potential benefits - and pitfalls - of modern microbial therapies, such as pre- and probiotics, faecal microbiota transplants, and microbial rewilding. We discuss the limited, yet growing, empirical evidence for the use of microbial therapies to modulate animal gut microbiomes beneficially. Interspersed throughout, we propose 12 actionable steps, grounded in evolutionary medicine, that can be applied to practical animal care and management. We encourage that these actionable steps be paired with integration of eco-evolutionary perspectives into our definitions of appropriate animal care standards. The evolutionary perspectives proposed herein may be best appreciated when applied to the broad diversity of species under human care, rather than when solely focused on humans. We urge animal care professionals, veterinarians, nutritionists, scientists, and others to collaborate on these efforts, allowing for simultaneous care of animal patients and the generation of valuable empirical data.

A physiologically based model of bile acid metabolism in mice

Bile acid (BA) metabolism is a complex system that includes a wide variety of primary and secondary, as well as conjugated and unconjugated BAs that undergo continuous enterohepatic circulation (EHC). Alterations in both composition and dynamics of BAs have been associated with various diseases. However, a mechanistic understanding of the relationship between altered BA metabolism and related diseases is lacking. Computational modeling may support functional analyses of the physiological processes involved in the EHC of BAs along the gut-liver axis. In this study, we developed a physiologically based model of murine BA metabolism describing synthesis, hepatic and microbial transformations, systemic distribution, excretion, and EHC of BAs at the whole-body level. For model development, BA metabolism of specific pathogen-free (SPF) mice was characterized in vivo by measuring BA levels and composition in various organs, expression of transporters along the gut, and cecal microbiota composition. We found significantly different BA levels between male and female mice that could only be explained by adjusted expression of the hepatic enzymes and transporters in the model. Of note, this finding was in agreement with experimental observations. The model for SPF mice could also describe equivalent experimental data in germ-free mice by specifically switching off microbial activity in the intestine. The here presented model can therefore facilitate and guide functional analyses of BA metabolism in mice, e.g., the effect of pathophysiological alterations on BA metabolism and translation of results from mouse studies to a clinically relevant context through cross-species extrapolation.

Validation of complementary non-invasive tools for stress assessment in spotted paca (Cuniculus paca)

Monitoring the concentration of glucocorticoid metabolites (GCMs) in faecal samples is a non-invasive tool for physiological stress evaluation, particularly useful when studying wild species. However, both negative and positive stimuli (distress and eustress, respectively) can lead to a rise in glucocorticoids. Thus, besides validating whether GCM concentration in faeces reflects endogenous adrenal activity, we also need to identify behavioural indicators of distress to avoid misinterpretation. Therefore, we submitted four adult male spotted pacas (Cuniculus paca) to an exogenous adrenocorticotropic hormone (ACTH) challenge-test in a Latin square design (4 × 4) to monitor changes in the GCM concentration in faeces. We also aimed to describe behaviours potentially indicative of distress. We collected excreted faeces and video-recorded the animals' behaviours for five consecutive days, one day before and four days after application of the following four treatments: 1st control (no-handling); 2nd control (intra-muscular [IM] injection of saline solution); low-dose ACTH (IM injection of 0.18 ml ACTH); and high-dose ACTH (IM injection of 0.37 ml ACTH). There was a peak in the concentration of GCM in faeces collected 24 h after the injection of the high-dose ACTH treatment. Additionally, independent of the treatments, spotted pacas spent less time on exploration and feeding states, while spending more time in the inactive but awake (IBA) state following the treatment application (challenge day). The use of GCM concentration in faecal samples together with the behavioural changes (less exploration and feeding, and more IBA) showed to be efficient as a non-invasive tool for welfare assessment of farmed spotted paca.

Comparative gastrointestinal organ lengths among Amazonian primates (Primates: Platyrrhini)

OBJECTIVES

The morphological features of the gastrointestinal tract (GIT) in mammals reflect a species' food niche breadth and dietary adaptations. For many wild mammals, the relationship between the structure of the GIT and diet is still poorly understood, for example, the GIT for frugivorous primates is usually classified as unspecialized and homogeneous. Here, we compare the GIT structure of 13 primate species from the three families of extant platyrrhines (Atelidae, Pitheciidae, and Cebidae) in Amazonia, and discuss possible evolutionary adaptations to different diets and trophic niches.

METHODS

We measured the length of the esophagus, stomach, small intestine, large intestine, cecum, colon, and rectum of the digestive tracts of 289 primate specimens. We determined the allometric relationships of the different tubular organs with the total length of the GIT as a proxy of specimen body size. Allometric parameters were used to establish the quotients of differentiation of every organ for each primate specimen.

RESULTS

There was a high differentiation in structure of the digestive organs among genera. Alouatta specimens clearly separated from the other genera based on dissimilarities in gastric, colonic, and rectal quotients, likely linked to the fermentation of plant contents. In contrast, all cebines (Sapajus, Cebus, and Saimiri) and Cacajao species had similar small intestine quotients, which is expected due to their high rates of animal matter consumed.

CONCLUSIONS

We show that diverse adaptations in digestive structure exist among frugivorous primates, which in turn reflect different dietary patterns within this group that may enable the geographic coexistence of different primate species.

Coprophagy Prevention Decreases the Reproductive Performance and Granulosa Cell Apoptosis via Regulation of CTSB Gene in Rabbits

Coprophagy is an instinctive behavior in rabbit with important effects on growth and reproductive performance. The underlying mechanism of this effect in rabbit is unknown. Here, we used Elizabeth circle as a coprophagy preventing model in female rabbits and assess feed intake, growth, and reproductive performance. We found that preventing coprophagy did not affect feed intake but decreased body weight and weight of several organs and tissues and resulted in complete reproductive failure during the late pregnancy period, accompanied by reduced levels of plasma progesterone. RNA-seq analysis of rabbit ovarian tissues revealed that preventing coprophagy affected significantly 241 genes (DEGs), with the large majority being downregulated. Bioinformatic analyses revealed that those DEGs are mostly involved in apoptosis, immune response, and metabolic pathways. Among DEGs, the lysosomal cysteine protease cathepsin B (CTSB) was significantly downregulated in the coprophagy prevention group. Further studies using siRNA and adenovirus overexpression systems revealed that CTSB promotes the proliferation of rabbit granulosa cells (GCS) and prevents apoptosis. Measurement of transcripts coding for proteins related to apoptosis revealed a minor transcriptomic effect of CTSB, indicating that its effect is likely post-transcriptional. Overexpression of CTSB increased secretion of progesterone and estradiol, partly via upregulation of CYP19A1 while inhibition of CTSB decreased progesterone secretion partly via downregulation of the StAR gene. In conclusion, our study demonstrated the detrimental effect on reproduction by preventing coprophagy with a main role for this response played by CTSB on the granulosa cells of the ovary.

Bacteria and Bellicosity: Photoperiodic Shifts in Gut Microbiota Drive Seasonal Aggressive Behavior in Male Siberian Hamsters

The existence of a microbiome-gut-brain axis has been established wherein gut microbiota significantly impacts host behavior and physiology, with increasing evidence suggesting a role for the gut microbiota in maintaining host homeostasis. Communication between the gut microbiota and the host is bidirectional, and shifts in the composition of the gut microbiota are dependent on both internal and external cues (host-derived signals, such as stress and immunity, and endocrine and environmental signals, such as photoperiod). Although there is host-driven seasonal variation in the composition of the microbiota, the mechanisms linking photoperiod, gut microbiota, and host behavior have not been characterized. The results of the present study suggest that seasonal changes in the gut microbiota drive seasonal changes in aggression. Implanting short-day Siberian hamsters (Phodopus sungorus) with fecal microbiota from long-day hamsters resulted in a reversal of seasonal aggression, whereby short-day hamsters displayed aggression levels typical of long-day hamsters. In addition, there are correlations between aggressive behavior and several bacterial taxa. These results implicate the gut microbiota as part of the photoperiodic mechanism regulating seasonal host behavior and contribute toward a more comprehensive understanding of the relationships between the microbiota, host, and environment.

Morphology of Starch Particles along the Passage through the Gastrointestinal Tract in Laboratory Mice Fed Extruded and Pelleted Diets

Simple Summary

Starch is the main carbohydrate source in most lab mouse diets. Its properties are influenced by feed processing. This determines how easily accessible it is to enzymatic digestion in the gastrointestinal tract of animals. In previous studies we have shown that there are differences between pelleted and extruded forms of a maintenance diet fed to mice regarding digestibility and microbiome. To complement these findings, the present study presents a morphological study of the starch particles throughout the passage along the gastrointestinal tract of C57BL/6J mice fed either pellets or extrudate. Samples were stained with Lugol’s iodine and examined via stereomicroscope and scanning electron microscope. Starch granules in the pelleted diet are mostly intact and compact, thus autoenzymatic digestion in the small intestine is less efficient than in the more accessible starch granules from the extruded diet. For both diet forms, starch accumulation in the caecum was observed, suggesting selective retention of praecaecally undigested starch for microbial fermentation. These findings allow for unique insights in murine starch digestion that are important to understand the digestive physiology of this species.

Abstract

Diet processing impacts on starch properties, such as the degree of starch gelatinization. This affects digestibility, as shown in laboratory mice fed either a pelleted or an extruded diet. In the present study, the morphology of starch particles throughout the digestive tract of mice was visualized. Thirty-two female C57BL/6J mice were used for a feeding trial. They were fed a commercial maintenance diet for laboratory mice, which was available in pelleted and extruded form, for seven weeks. The mice were sacrificed after the feeding period, and chyme samples were collected from five sites (stomach, anterior and posterior small intestine, caecum, colon). Samples of diets, chyme and faeces were analyzed via stereomicroscopy (stained with Lugol’s iodine) and scanning electron microscopy (SEM). The starch granules appeared more compact in the pelleted diet, showing first signs of degradation only in the small intestine. The caecum content of both diets group was intensively stained, particles as well as fluid phase, indicating that it contained mainly starch. The SEM pictures of caecum content showed abundant bacteria near starch particles. This suggests selective retention of prae-caecally undigested starch in the murine caecum, likely the site of microbial fermentation.

Homo-Acetogens: Their Metabolism and Competitive Relationship with Hydrogenotrophic Methanogens

Homo-acetogens are microbes that have the ability to grow on gaseous substrates such as H₂/CO₂/CO and produce acetic acid as the main product of their metabolism through a metabolic process called reductive acetogenesis. These acetogens are dispersed in nature and are found to grow in various biotopes on land, water and sediments. They are also commonly found in the gastro-intestinal track of herbivores that rely on a symbiotic relationship with microbes in order to breakdown lignocellulosic biomass to provide the animal with nutrients and energy. For this motive, the fermentation scheme that occurs in the rumen has been described equivalent to a consolidated bioprocessing fermentation for the production of bioproducts derived from livestock. This paper reviews current knowledge of homo-acetogenesis and its potential to improve efficiency in the rumen for production of bioproducts by replacing methanogens, the principal H₂-scavengers in the rumen, thus serving as a form of carbon sink by deviating the formation of methane into bioproducts. In this review, we discuss the main strategies employed by the livestock industry to achieve methanogenesis inhibition, and also explore homo-acetogenic microorganisms and evaluate the members for potential traits and characteristics that may favor competitive advantage over methanogenesis, making them prospective candidates for competing with methanogens in ruminant animals.

Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides

The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy.

Effects of dietary bamboo ( Phyllostachys pubescens Mazel) culm powder on blood properties and intestinal environment of rabbits

This study investigated the effects of bamboo powder as an alternative feed for rabbits. The normal hay diet of rabbits was replaced with bamboo culm powder (10% and 20%) and fed to the rabbits until they were 90 days old. The blood samples were collected when the rabbits were 46, 66, and 90 days old to assess the effects of bamboo powder on blood parameters. The organs and intestinal contents were harvested at the age of 90 days, and the functions and morphologies of different organs were evaluated. The concentration of short-chain fatty acids (SCFAs) and the composition of microbiota in the cecum were measured. Substituting bamboo powder did not affect the growth, hematology profile, intestinal morphologies, and cecum SCFA concentration in rabbits. In contrast, it significantly altered the cecum microbiota composition, particularly the abundance of Ruminococcus and Bacteroides related to fiber degradation and Tyzzerella spp., associated with large intestine inflammation. These findings suggest that the substitution of hay with bamboo powder in rabbit diets does not negatively affect the overall health of rabbits and could be considered an alternative feed for rabbits; nevertheless, the protein and lipid deficiency in the bamboo powder should be taken into account.

Effect of Sustained Administration of Thymol on Its Bioaccessibility and Bioavailability in Rabbits

Simple Summary

The purpose of this study was to investigate the bioavailability and metabolic path of thymol, a major constituent of Thymus vulgaris L., in the rabbit organism. Oral bioavailability is a key parameter affecting the efficacy of substances, but it is not surprising that it does not correlate satisfactorily with efficacy. The main limitation factors are rate of absorption, metabolism, and excretion processes. In this work, the thymol metabolic path in the rabbit organism was determined for the first time after its sustained oral administration. We confirm intensive absorption of thymol from the gastrointestinal tract; our results point to metabolism and accumulation in kidney tissue and intensive metabolic and excretion processes in the liver. Some metabolic processes were present also after thymol withdrawal. Thymol as a lipophilic substance was found only in trace amounts in fat and muscle tissue as a consequence of its conversion into hydrophilic metabolite and greater elimination in the rabbit organism. This paper highlights the insufficient knowledge of modes of action of plant compounds in animal organisms.

Abstract

The objective of this study was the detection of thymol in rabbit plasma, tissues, large intestinal content, and faeces. Forty-eight rabbits were divided into control and experimental groups (thymol 250 mg/kg feed). Thymol was administered for 21 days and then withdrawn for 7 days. Concentration of thymol in the intestinal wall (IW) was significantly higher than in plasma (p < 0.05) and liver (p < 0.05); in the kidneys it was significantly higher than in plasma (p < 0.05) and liver (p < 0.05) during thymol addition. Thymol in IW was significantly higher than in plasma also after withdrawal (p < 0.01). Significant correlation (r_s = −1.000, p < 0.01) between IW and plasma points to the intensive absorption of thymol from the intestine, while the correlation between plasma and liver (r_s = 0.786, p < 0.05) indicates intensive biotransformation and excretion processes in liver. Significant correlation between liver and kidney (r_s = 0.738, p < 0.05) confirms the intensive metabolism of thymol in the kidney. During the withdrawal period, thymol was detected above trace amounts only in faeces, and was significantly higher than in the colon during both periods (p < 0.01). Results show intensive biotransformation of thymol in the rabbit organism.

Oral administration of Moringa oleifera leaf powder relieves oxidative stress, modulates mucosal immune response and cecal microbiota after exposure to heat stress in New Zealand White rabbits

Background

Heat stress (HS) disrupts the gut barrier allowing the uptake of lipopolysaccharide (LPS) and leads to an inflammatory response and changes in gut microbiota composition. Moringa oleifera leaf powder (MOLP) has been proposed to combat HS, yet its alleviate role is currently under investigation. The current study investigated the effects of chronic HS and MOLP supplementation on changes in redox status and immune response of cecal mucosa along with alteration in cecal microbiota.

Methods

A total of 21 young New Zealand White (NZW) rabbits (male) about 32 weeks old (mean body weight of 3318 ± 171 g) reared on a commercial pelleted diet were employed; divided into three groups (n = 7): control (CON, 25 °C), heat stress (HS, 35 °C for 7 h daily), and HS supplemented orally with MOLP (HSM, 35 °C) at 200 mg/kg body weight per day for 4 weeks.

Results

The results demonstrated that MOLP supplementation increased organ index of cecal tissue compared with the HS group (P > 0.05). Levels of malonaldehyde (MDA) and activity of superoxide dismutase (SOD) as well as lactate dehydrogenase (LDH) were reduced in the cecal mucosa of the HSM group compared with the HS group. MOLP downregulated the contents of cecal mucosa LPS, several inflammatory markers (TNF-α/IL-1α/IL-1β), and myeloperoxidase (MPO) in the HSM group (P < 0.05). Secretory immunoglobulin A (SIgA) was increased in the HSM group compared with the HS group (P < 0.05). The transcriptome of cecal mucosa showed that MOLP reduced gene expression relative to several immune factors, including IL-10, IFNG, and RLA, whereas both HS and MOLP increased the gene expression of fat digestion and absorption pathway, including APOA1, FABP1, FABP2, MTTP, and LOC100344166, compared to the CON group (P < 0.001). At the phylum level, the relative abundance of Proteobacteria was increased by HS, while Actinobacteria was significantly increased by HSM compared to other groups (P < 0.05). At genus level, Papillibacter was higher in abundance in HSM groups compared to CON and HS groups (P < 0.05). Higher butyrate concentrations were observed in the HSM group than HS and CON groups (P < 0.05).

Conclusion

In conclusion, HS in growing rabbits resulted in alteration of cecal microbiota at phyla level as well as increased oxidative stress and expression of mucosal inflammatory genes. Whereas, oral MOLP supplementation elevated the relative weight of cecum, affected their immunological and cecal micro-ecosystem function by improving antioxidant status and down-regulating mucosal tissue inflammatory response.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00586-y.

Unique Running Pattern and Mucosal Morphology Found in the Colon of Cotton Rats

Cotton rats are one of the experimental rodents used for testing different infectious and non-infectious diseases, including gastrointestinal tract pathology. However, their intestinal morphological characteristics are still poorly understood. Here, we clarified the anatomical and histological characteristics of the cecum and ascending colon (AC) of young (1–3-month old), adult (4–6-month old), and old (10–12-month old) cotton rats. The large intestine (LI) in cotton rats is composed of the cecum, AC, transverse and descending colons, and rectum, and is similar to that of other mammals. The AC begins with a double or triple spiral loop-like flexure (SLLF) and ends with a coupled horseshoe-like flexure (HSLF). A single longitudinal mucosal fold (SLMF) was found at the beginning of the AC along the mesentery line and developed with age. Furthermore, the SLMF contained several lymphatic nodules (LNs), indicating their role in digestive and immunological functions. Small and large protuberant LNs were found in the cecum and SLLF, respectively, whereas thin and flat LNs were observed in the HSLF and transverse colon, respectively. Regarding sex-related differences, adult females had a significantly longer AC with a higher number of SLLFs compared to males. The SLMF length and LN number were also longer and higher, respectively, in adult females compared to adult males. These are crucial findings, indicating the presence of sex-related differences in the morphology of the LI in cotton rats, and ours is the first study to discover a sex difference in the mammalian LI lining. Our study clarified the unique morphology of the LI in cotton rats, which could serve as the principal model for elucidating species-specific digestive tract functions and gastrointestinal disorders.

Of men in mice: the development and application of a humanized gnotobiotic mouse model for microbiome therapeutics

Considerable evidence points to the critical role of the gut microbiota in physiology and disease. The administration of live microbes as a therapeutic modality is increasingly being considered. However, key questions such as how to identify candidate microorganisms and which preclinical models are relevant to recapitulate human microbiota remain largely unanswered. The establishment of a humanized gnotobiotic mouse model through the fecal microbiota transplantation of human feces into germ-free mice provides an innovative and powerful tool to mimic the human microbial system. However, numerous considerations are required in designing such a model, as various elements, ranging from the factors pertaining to human donors to the mouse genetic background, affect how microbes colonize the gut. Thus, it is critical to match the murine context to that of human donors to provide a continuous and faithful progression of human flora in mice. This is of even greater importance when the need for accuracy and reproducibility across global research groups are taken into account. Here, we review the key factors that affect the formulation of a humanized mouse model representative of the human gut flora and propose several approaches as to how researchers can effectively design such models for clinical relevance.

Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research

The interaction between nutrition and human infectious diseases has always been recognized. With the emergence of molecular tools and post-genomics, high-resolution sequencing technologies, the gut microbiota has been emerging as a key moderator in the complex interplay between nutrients, human body, and infections. Much of the host-microbial and nutrition research is currently based on animals or simplistic in vitro models. Although traditional in vivo and in vitro models have helped to develop mechanistic hypotheses and assess the causality of the host-microbiota interactions, they often fail to faithfully recapitulate the complexity of the human nutrient-microbiome axis in gastrointestinal homeostasis and infections. Over the last decade, remarkable progress in tissue engineering, stem cell biology, microfluidics, sequencing technologies, and computing power has taken place, which has produced a new generation of human-focused, relevant, and predictive tools. These tools, which include patient-derived organoids, organs-on-a-chip, computational analyses, and models, together with multi-omics readouts, represent novel and exciting equipment to advance the research into microbiota, infectious diseases, and nutrition from a human-biology-based perspective. After considering some limitations of the conventional in vivo and in vitro approaches, in this review, we present the main novel available and emerging tools that are suitable for designing human-oriented research.

Diminished enteric neuromuscular transmission in the distal colon following experimental spinal cord injury

Neurogenic bowel following spinal cord injury (SCI) leads to decreased colonic motility, remodeling of the neuromuscular compartment and results in chronic evacuation difficulties. The distal colon of the rat serves a dual role for fluid absorption and storage that is homologous to the descending colon of humans. Dysmotility of the descending colon is one component of neurogenic bowel. We investigated the integrity of the enteric neuromuscular transmission responsible for the generation of excitatory and inhibitory junction potentials (EJPs and IJPs, respectively) in the distal colon of rats. We previously demonstrated a chronic reduction in colonic enteric neurons from rats with acute and chronic high-thoracic (T3) SCI and hypothesized that neurogenic bowel following T3-SCI results from diminished enteric neuromuscular transmission. Immunohistochemical labeling for myenteric neuronal nitric oxide synthase (nNOS) and choline acetyltransferase (ChAT) neurons demonstrated a significant loss of presumptive nitric oxide (NO) and acetylcholine (ACh) immunoreactive neurons in both 3-day and 3-week injured animals. Colonic neuromuscular transmission in response to transmural electrical stimulation of the colon was significantly reduced 3-days and 3-weeks following SCI in male rats. Specifically, cholinergic-mediated excitatory junction potentials (EJPs) and nitrergic-mediated slow inhibitory junction potentials (IJPs) were significantly reduced while ATP-mediated fast IJPs remained unaffected. We conclude that a reduction in excitatory and inhibitory enteric neuromuscular transmission contributes to neurogenic bowel observed following SCI, and that these loss-of-function changes involve enteric-mediated cholinergic and nitrergic pathways.

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels

Thermal homeostasis of mammals is constrained by body-size scaling. Consequently, small mammals require considerable energy to maintain a high mass-specific metabolic rate (MSMR) and sustain target body temperature. In association with gut microbiota, mammalian hosts acquire absorbable molecules and fulfill their metabolic requirements. Our objective was to characterize gut microbes in wild mammals and relate those findings to host body-size scaling. Two large (Petaurista philippensis grandis and P. alborufus lena), one medium (Trogopterus xanthipes) and one small (Pteromys volans orii) species of flying squirrels (FS) were studied. Using 16S rRNA genes, 1,104 OTUs were detected from four FS, with 1.99% of OTUs shared among all FS. Although all FS gut microbiota were dominated by Firmicutes, they were constituted by different bacterial families. Moreover, Bacteroidetes accounted for up to 19% of gut microbiota in small FS, but was absent in large FS. Finally, based on metagenome predictions, carbohydrate and amino acid metabolism genes were enriched in small body-size FS. In conclusion, gut microbiota compositions and predictive metabolic functions were characteristic of body-size in FS, consistent with their adaptations to folivorous dietary niches.

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana

The grasscutter (also known as the greater cane rat; Thryonomys swinderianus) is a large rodent native to West Africa that is currently under domestication process for meat production. However, little is known about the physiology of this species. In the present study, aiming to provide information about gut microbiota of the grasscutter and better understand its physiology, we investigated the intestinal microbiota of grasscutters and compared it with that of other livestock (cattle, goat, rabbit, and sheep) using 16S rRNA metagenomics analysis. Similar to the other herbivorous animals, bacteria classified as Bacteroidales, Clostridiales, Ruminococcaceae, and Lachnospiraceae were abundant in the microbiome of grasscutters. However, Prevotella and Treponema bacteria, which have fiber fermentation ability, were especially abundant in grasscutters, where the relative abundance of these genera was higher than that in the other animals. The presence of these genera might confer grasscutters the ability to easily breakdown dietary fibers. Diets for grasscutters should be made from ingredients not consumed by humans to avoid competition for resources and the ability to digest fibers may allow the use of fiber-rich feed materials not used by humans. Our findings serve as reference and support future studies on changes in the gut microbiota of the grasscutter as domestication progresses in order to establish appropriate feeding methods and captivity conditions.

Influence of cecotrophy on fat metabolism mediated by caecal microorganisms in New Zealand white rabbits

Cecotrophy is a special behaviour of rabbits. Eating soft faeces can improve feed efficiency and maintain gut flora in rabbits. In our previous study, we found that fasting from soft faeces significantly reduced growth rate and total cholesterol (TC) in New Zealand white rabbits (NZW rabbits), thereby resulting in lower values for body weight and fat deposition in the soft faeces fasting group than in the control group. However, it has not been demonstrated whether cecotrophy by NZW rabbits can regulate lipid metabolism by changing the diversity of caecal microorganisms. In this study, thirty-six 28-day-old weaned NZW female rabbits were randomly divided into two groups (the soft faeces fasting group and the control group) and fed to 90 days. Rabbits in the experimental group were treated with an Elizabeth circle to prevent them from eating their soft faeces. Then, the caecal contents of three rabbits from the soft faeces fasting group and three rabbits from the control group were collected for metagenomic sequencing. We found that the abundance of Bacteroides increased, while Ruminococcus decreased, compared with the control group after fasting from soft faeces. Relative abundance was depressed for genes related to metabolic pathways such as ascorbate and aldarate metabolism, riboflavin metabolism and bile secretion. Moreover, there was a general correlation between variation in microbial diversity and fat deposition. Bacteroides affects body weight and TC by participating in the riboflavin metabolism pathway. By investigating the effect of cecotrophy on caecal microorganisms of rabbits, we identified the key microorganisms that regulate the rapid growth performance of NZW rabbits, which may provide useful reference for the future research and development of microecological preparations for NZW rabbits.

Energy requirements, length of digestive tract compartments and body mass in six gerbilline rodents of the Negev Desert

Energy requirements of an animal are size dependent and, in this study, the average daily metabolic rate (ADMR) of six Negev Desert gerbilline rodents, ranging in body mass (m_b) from 10g to over 200g, scaled to m_b^0.57. Although gerbilline rodents are considered 'granivores', these rodents consume substantial amounts of green vegetation and the largest gerbil is a strict herbivore. We predicted that the lengths of the compartments of the digestive tract would scale allometrically to mb^0.33 and that ADMR would scale allometrically to the lengths of the compartments to the exponent of 1.73. Using log-transformed data, the length of the colon scaled to m_b^0.50 (r²_adj = 0.74; p= 0.02), of the caecum to m_b^0.45 (r²_adj=0.80; p= 0.01) and of the small intestine to m_b^0.30 (r²_adj=0.59; p < 0.05). Therefore, the exponents for the colon and caecum were higher than predicted and were close to the exponent for ADMR generated for the rodents. The absolute lengths of the colon (r²_adj=0.68; p= 0.03; slope = 0.99) and of the caecum (r²_adj=0.79; p= 0.01; slope = 1.19) were related significantly to ADMR, but of the small intestine was not (r²_adj=0.04; p=0.33; slope = 0.85). The exponents implied that the relationships were isometric and not allometric as predicted and that the rates of increase of the lengths of the intestine compartments were at the same rate as the increase in ADMR. The lengths of the colon and caecum were highly correlated between each other (r²_adj=0.98; p< 0.001; slope = 1.12) and explained most of the variation in ADMR. Green vegetation could be a nutritional bottleneck for rodents as it is bulky and, consequently, limits the dietary intake, and fermentation occurs in the caecum and colon, whereas seeds, which are compact and are digested in the small intestine, would limit intake to a much lesser degree. However, when the effect of body mass was eliminated by using residuals of the variables on body mass, only the length of the small intestine was significant (r²_adj=0.86; p< 0.005; slope = -1.33) and was related negatively to ADMR. Therefore, when effects of body size were removed, most of the variation in ADMR was explained by the length of the small intestine and implied that the length of the small intestine increased with a decrease in ADMR. A higher energy expenditure was related to a shorter small intestine and, therefore, by implication, a higher concentration of metabolizable energy yield of the diet. We also questioned whether there are differences in the morphology of the digestive tract due to differences in dietary consumption. The digestive tracts of the gerbils were not diverse and could be characterized as structurally homogenous. All the gerbils had a uni-locular, hemi-glandular stomach and the differences in the digestive tract among species did not seem to be of functional importance, but rather were related to the taxon. However, some important morpho-functional characteristics of the digestive tract emerged that apply to the whole group.

The effect of fish and mealworm larvae meals as alternative dietary protein sources on nutrient digestibility and gastrointestinal function in Chinchilla lanigera

Chinchillas are herbivores, but wild chinchillas may occasionally consume animal-based foods. The aim of this study was to determine the effect of fish meal (FM) and mealworm meal (MWM) included in complete pelleted diets on nutrient digestibility and gastrointestinal function in chinchillas. The experiment was performed on 24 male, divided into three groups, n=8. Control group (C) was fed a diet containing 10% soybean meal (SBM). In the experimental group FM, chinchillas received a diet containing 3% fish meal, and the diet administered to the experimental group MWM was supplemented with 4% dried mealworm larvae meal. The nutrient digestibility of diets was determined. At the end of the experiment animals were euthanized and their digestive tracts were removed to analyze gut activity. FM group animals were characterized by lower crude fat digestibility, whereas both alternative protein sources improved the digestibility of acid detergent fiber (ADF). A considerable increase in the activity of cecal intracellular and extracellular bacterial enzymes (in particular β-glucosidase, β-galactosidase and β-xylosidase) was noted in the FM group, which however did not increase the concentrations of short-chain fatty acids (SCFA). The inclusion of MWM in chinchilla diets shifted the bacterial fermentation site from the cecum (lowest SCFA pool) to the colon (highest SCFA pool), thus enabling to derive additional energy from less digestible dietary components. In conclusion, chinchilla diets can be supplemented with small amounts of animal protein such as fish meal and dried mealworm larvae meal.

Analysis of glycoconjugates and morphological characterization of the descending colon and rectum of the plains viscacha, Lagostomus maximus

Herbivores exhibit specializations at the intestinal level that facilitate the bacterial fermentation. The available information on the digestive physiology of Lagostomus maximus makes this rodent an interesting model to evaluate morpho-functional adaptations to herbivory. The general objective of this work was centered on the study of the morphology and histochemistry of the descending colon and rectum of L. maximus. To do so, a comparative analysis of the morphology, ultrastructure and glycosylation pattern of both anatomical regions was carried out. Histochemical results revealed that in both sectors of the large intestine, there are goblet cells with different glycosylation pattern within a morphologically homogeneous cell population. The main difference between both intestinal segments lay in the fact that the most distal region of the large intestine showed a greater proportion of sialomucins, characterized by being slightly O-acetylated. Further specific differences were revealed by lectin histochemistry. These data allowed to perform a functional interpretation of the cell types and secreted substances, thus contributing to a better understanding of the role of mucins in the intestinal tract functioning.

Comparative cytology, physiology and transcriptomics of Burkholderia insecticola in symbiosis with the bean bug Riptortus pedestris and in culture

In the symbiosis of the bean bug Riptortus pedestris with Burkholderia insecticola, the bacteria occupy an exclusive niche in the insect midgut and favor insect development and reproduction. In order to understand how the symbiotic bacteria stably colonize the midgut crypts and which services they provide to the host, we compared the cytology, physiology, and transcriptomics of free-living and midgut-colonizing B. insecticola. The analyses revealed that midgut-colonizing bacteria were smaller in size and had lower DNA content, they had increased stress sensitivity, lost motility, and an altered cell surface. Transcriptomics revealed what kinds of nutrients are provided by the bean bug to the Burkholderia symbiont. Transporters and metabolic pathways of diverse sugars such as rhamnose and ribose, and sulfur compounds like sulfate and taurine were upregulated in the midgut-colonizing symbionts. Moreover, pathways enabling the assimilation of insect nitrogen wastes, i.e. allantoin and urea, were also upregulated. The data further suggested that the midgut-colonizing symbionts produced all essential amino acids and B vitamins, some of which are scarce in the soybean food of the host insect. Together, these findings suggest that the Burkholderia symbiont is fed with specific nutrients and also recycles host metabolic wastes in the insect gut, and in return, the bacterial symbiont provides the host with essential nutrients limited in the insect food, contributing to the rapid growth and enhanced reproduction of the bean bug host.

Deconstructing the physical processes of digestion: reductionist approaches may provide greater understanding

I provide a broad overview of the physical factors that govern intestinal digestion i.e. the admixture of food particles in digesta with secreted enzymes and the subsequent mass transfer of liberated nutrients from the surfaces of particles to the gut wall, with a view to outlining the quantitative work that is required to determine the relative importance of these factors in the digestion of particular foods. I first discuss what is known of the mechanical forces generated by contraction of the walls of the various segments of the gut and the level of diffusive, and advective mixing that it generates within the lumen. I then discuss the particular physical effects that may limit the digestion of solid, physically and/or chemically homogenous and heterogeneous food particles, notably capillarity, porosity, poro-elastic flow and compaction and their likely effects on diffusive and convective mass transfer at particulate surfaces. Similarly, I discuss mucins and morphology on mass transfer of nutrients to the gut wall i.e. the mucosa.

Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs

Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring's adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father's LPD treatment in both, liver and testis tissues. Our results point to a 'heritable epigenetic response' of the sons to the fathers' dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming ('metabolic shift'). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change.

Anatomical and Functional Changes to the Colonic Neuromuscular Compartment after Experimental Spinal Cord Injury

A profound reduction in colorectal transit time accompanies spinal cord injury (SCI), yet the colonic alterations after SCI have yet to be understood fully. The loss of descending supraspinal input to lumbosacral neural circuits innervating the colon is recognized as one causal mechanism. Remodeling of the colonic enteric nervous system/smooth muscle junction in response to inflammation, however, is recognized as one factor leading to colonic dysmotility in other pathophysiological models. We investigated the alterations to the neuromuscular junction in rats with experimental high-thoracic (T3) SCI. One day to three weeks post-injury, both injured and age-matched controls underwent in vivo experimentation followed by tissue harvest for histological evaluation. Spontaneous colonic contractions were reduced significantly in the proximal and distal colon of T3-SCI rats. Histological evaluation of proximal and distal colon demonstrated significant reductions of colonic mucosal crypt depth and width. Markers of intestinal inflammation were assayed by qRT-PCR. Specifically, Icam1, Ccl2 (MCP-1), and Ccl3 (MIP-1α) mRNA was acutely elevated after T3-SCI. Smooth muscle thickness and collagen content of the colon were increased significantly in T3-SCI rats. Colonic cross sections immunohistochemically processed for the pan-neuronal marker HuC/D displayed a significant decrease in colonic enteric neuron density that became more pronounced at three weeks after injury. Our data suggest that post-SCI inflammation and remodeling of the enteric neuromuscular compartment accompanies SCI. These morphological changes may provoke the diminished colonic motility that occurs during this same period, possibly through the disruption of intrinsic neuromuscular control of the colon.

Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling

Mammalian herbivores rely on microbial activities in an expanded gut chamber to convert plant biomass into absorbable nutrients. Distinct from ruminants, small herbivores typically have a simple stomach but an enlarged cecum to harbor symbiotic microbes; however, knowledge of this specialized gut structure and characteristics of its microbial contents is limited. Here, we used leaf-eating flying squirrels as a model to explore functional characteristics of the cecal microbiota adapted to a high-fiber, toxin-rich diet. Specifically, environmental conditions across gut regions were evaluated by measuring mass, pH, feed particle size, and metabolomes. Then, parallel metagenomes and metatranscriptomes were used to detect microbial functions corresponding to the cecal environment. Based on metabolomic profiles, >600 phytochemical compounds were detected, although many were present only in the foregut and probably degraded or transformed by gut microbes in the hindgut. Based on metagenomic (DNA) and metatranscriptomic (RNA) profiles, taxonomic compositions of the cecal microbiota were dominated by bacteria of the Firmicutes taxa; they contained major gene functions related to degradation and fermentation of leaf-derived compounds. Based on functional compositions, genes related to multidrug exporters were rich in microbial genomes, whereas genes involved in nutrient importers were rich in microbial transcriptomes. In addition, genes encoding chemotaxis-associated components and glycoside hydrolases specific for plant beta-glycosidic linkages were abundant in both DNA and RNA. This exploratory study provides findings which may help to form molecular-based hypotheses regarding functional contributions of symbiotic gut microbiota in small herbivores with folivorous dietary habits.

Mouse models for human intestinal microbiota research: a critical evaluation

Since the early days of the intestinal microbiota research, mouse models have been used frequently to study the interaction of microbes with their host. However, to translate the knowledge gained from mouse studies to a human situation, the major spatio-temporal similarities and differences between intestinal microbiota in mice and humans need to be considered. This is done here with specific attention for the comparative physiology of the intestinal tract, the effect of dietary patterns and differences in genetics. Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity. Moreover, a large variety of murine strains is available yet most of the microbiota research is performed in wild-type, inbred strains and their transgenic derivatives. It has become increasingly clear that the providers, rearing facilities and the genetic background of these mice have a significant impact on the microbial composition and this is illustrated with recent experimental data. This may affect the reproducibility of mouse microbiota studies and their conclusions. Hence, future studies should take these into account to truly show the effect of diet, genotype or environmental factors on the microbial composition.

The colonic groove of the plains viscacha (Lagostomus maximus): Histochemical evidence of an abrupt change in the glycosylation pattern of goblet cells

The ascending colon of most rodent species shows a longitudinal colonic groove that works as a retrograde transport pathway for a mixture of bacteria and mucus toward the cecum. We describe the morphology and glycosylation pattern of the colonic groove of Lagostomus maximus to analyze the role of mucins in this anatomical feature. We also studied the distribution pattern of the interstitial cells of Cajal (ICC) to evaluate their regulatory influence on gut motility. The groove originated near the cecocolic junction and extended along the mesenteric side of the ascending colon, limited at both ends by nonpapillated ridges. These ridges divided the lumen of the ascending colon into two compartments: a narrow channel and a large channel, called the groove lumen and the main lumen, respectively. The histochemical analysis showed differences in the glycosylation pattern of the goblet cells inside and outside the groove. Unlike the mucosa lining the main lumen of the colon, the groove was rich in goblet cells that secrete sulfomucins. The PA/Bh/KOH/PAS technique evidenced an abrupt change in the histochemical profile of goblet cells, which presented a negative reaction in the groove and a strongly positive one in the rest of the colonic mucosa. The anti-c-kit immunohistochemical analysis showed different ICC subpopulations in the ascending colon of L. maximus. Of all types identified, the ICC-SM were the only cells located solely within the colonic groove.

Comparative gastrointestinal morphology of Tachyoryctes splendens (Rüppell, 1835) and Heliophobius emini, (Noack, 1894) two species of East African mole-rats

Tachyoryctes splendens (Northeast African mole-rat) and Heliophobius emini (Emin's mole-rat) are two African mole-rats that represent separate allopatric rodent families namely Spalacidae and Bathyergidae respectively. While these species consume a similar diet of underground plant storage organs such as roots and tubers, T. splendens has been reported to additionally consume small amounts of aerial foliage. This study aims to provide detailed gross morphological and histological morphometric analyses of the gastrointestinal tract (GIT) of these two subterranean species. The formalin fixed gastrointestinal tracts of T. splendens (n = 9) and H. emini (n = 6) were photographed, weighed and measured. The length and basal surface areas were calculated for each anatomically distinct region. Representative histological samples were prepared and stained using Hematoxylin and Eosin. Microscopic luminal measurements were used to calculate a surface enlargement factor and the luminal surface area of each region. Tachyoryctes splendens had a large double chambered hemi-glandular stomach with a macroscopically visible transition from keratinized stratified squamous epithelium to glandular epithelium. The cecum was large and the luminal surface revealed a single spiral fold. The ascending colon of T. splendens was arranged in a spiral, with two centripetal and two centrifugal windings. The descending colon was arranged in a single parallel loop, similar to H. emini. A narrow colonic groove was accompanied by V-shaped folds on either side. Heliophobius emini had a simple glandular stomach, a large, haustrated cecum that displayed a cecal appendix and the descending colon was arranged in a single parallel loop. The internal aspect of the colon revealed a wide colonic groove extending from the ceco-colic junction to distal colon. As both species originate from a similar geographical region and ingest very similar diets, it is likely that the differences in the GIT morphology are attributed to phylogeny as the species represent two different families of mole-rats.

Nutritional consequences of folivory in a small-bodied lemur (Lepilemur leucopus): Effects of season and reproduction on nutrient balancing

OBJECTIVES

Small-bodied folivores are rare because processing leaves often requires extensive gut adaptations and lengthy retention times for fiber fermentation. However, the <1 kg nocturnal white-footed sportive lemurs (Lepilemur leucopus) persist on a leaf-based diet. We investigated how extrinsic (i.e., seasonality in temperature and food availability) and intrinsic factors (i.e., reproductive state) influence nutrient intake and explored how nutrient and energy needs are met in this species.

MATERIALS AND METHODS

We conducted full night focal follows across all seasons and analyzed nutrients in all items eaten by adults of both sexes to investigate nutrient intake and nutritional priorities in L. leucopus. We estimated digestible protein content, as this is a biologically more meaningful measure than crude protein.

RESULTS

Protein intake was constant across seasons, while non-protein energy and dry matter intake increased from the hot wet to the cold dry season. Males and females did not differ in their nutrient or apparent energy intake irrespective of female reproductive state.

DISCUSSION

We conclude that these animals prioritize protein over non-protein energy intake as dietary protein is in limited supply, and that thermoregulation poses higher energetic costs than reproduction in this species. While protein intake did not differ across female reproductive states, the relative protein content of the diet was highest during the lactation period, indicating that the balance of non-protein to protein intake may be more important than absolute intake. Dry matter intake was high compared to other folivorous primates, indicating that L. leucopus follows an intake rather than an efficiency strategy to meet its energy requirements. Am J Phys Anthropol 160:197-207, 2016. © 2016 Wiley Periodicals, Inc.

Gut Function-Enhancing Properties and Metabolic Effects of Dietary Indigestible Sugars in Rodents and Rabbits

Indigestible sugars (iS) have received particular interest in food and nutrition research due to their prebiotic properties and other health benefits in humans and animals. The main aim of this review article is to summarize the current knowledge regarding digestive and health-enhancing properties of iS such as sugar alcohols, oligosacharides, and polysaccharides, in rodents and rabbits. Besides ameliorating gut health, iS ingestion also elicits laxative effects and stimulate intestinal permeability and fluid secretions, thereby shortening digesta transit time and increasing stool mass and quality. In rodents and rabbits, as hindgut fermenters, consumption of iS leads to an improved nutrient digestibility, too. Cecal fermentation of iS reduces luminal pH and extends wall tissue facilitating absorption of key dietary minerals across hindgut. The microbial fermentation of iS also enhances excessive blood nitrogen (N) flowing into the cecum to be used as N source for bacterial growth, enhancing N retention in cecotrophic animals. This review also highlights the impact of iS on improving lipid metabolism, mainly by lowering cholesterol and triglycerides levels in the blood. The paper serves as an index of the current knowledge of iS effects in rodents and rabbits and also identifies gaps of knowledge that need to be addressed by future research.

Host litter-associated gut dynamics affect Escherichia coli abundance and adhesion genotype in rats

The probability of detecting Escherichia coli varies between host species with different diets and body sizes. An experimental study that mimicked the effect of different carnivore body masses found that digesta transit times influence E. coli abundance. In this study, we investigated how the host's gastrointestinal dynamics affected E. coli abundance and genotype in a system that reflected an herbivorous host. Forty rats from nine litters were fed a diet high in fermentable fibre. We found a small effect of fibre concentration on the difference between the liquid and particle digesta retention times. However, the rats' litter membership explained the majority of the retention time differences (79%). In turn, we found that as the difference between liquid and particle retention times increased, E. coli faecal cell densities decreased, while the likelihood that an animal's dominant E. coli strain possessed a gene involved in adhesion (agn43) increased. Thus, this experiment revealed an unanticipated high degree of association between the hosts' litter, their gastrointestinal dynamics and the E. coli genotypes. Furthermore, by comparing our findings to previous work, we show that the presence of fermentable fibre in the diet appears to change the relationship between the host's phenotype and E. coli.

Fecal nitrogen concentration as a nutritional quality indicator for European rabbit ecological studies

Measuring the quality of the nutritional resources available to wild herbivores is critical to understanding trophic regulation processes. However, the direct assessment of dietary nutritional characteristics is usually difficult, which hampers monitoring nutritional constraints in natural populations. The feeding ecology of ruminant herbivores has been often assessed by analyzing fecal nitrogen (FN) concentrations, although this method has been less evaluated in other taxa. This study analyzed the suitability of FN as an indicator of ingesta quality in the European rabbit (Oryctolagus cuniculus), which is a keystone lagomorph species in Mediterranean ecosystems and of great conservation interest. Firstly, domestic O. cuniculus were used to evaluate under experimental conditions the accuracy of total FN and the metabolic FN as diet quality indicators of forages with characteristics similar to those available under natural conditions. Secondly, the accuracy of Near-Infrared Spectroscopy (NIRS) to calculate FN was tested using partial least squares regression. Thirdly, a pilot field study was conducted to monitor FN dynamics from wild O. cuniculus in three different habitats during wet and drought periods. A strong association was found between diet type and total FN and metabolic FN (Pseudo-R(2) ≥ 0.89). It was also found that NIRS calibrations were accurate for depicting nitrogen concentrations (R(2) > 0.98 between NIRS and chemical results). Finally, the seasonal FN dynamics measured in the field were consistent with current knowledge on vegetation dynamics and forage limitations in the three habitats. The results support the use of NIRS methods and FN indices as a reliable and affordable approach to monitoring the nutritional quality of rabbit habitats. Potential applications include the assessment of the mechanistic relationships between resource limitations and population abundance, e.g., in relation to natural drought cycles and to habitat interventions aimed at reinforcing rabbit populations.

Diet of worms emended: an update of polychaete feeding guilds

Polychaetes are common in most marine habitats and dominate many infaunal communities. Functional guild classification based on taxonomic identity and morphology has linked community structure to ecological function. The functional guilds now include osmotrophic siboglinids as well as sipunculans, echiurans, and myzostomes, which molecular genetic analyses have placed within Annelida. Advances in understanding of encounter mechanisms explicitly relate motility to feeding mode. New analyses of burrowing mechanics explain the prevalence of bilateral symmetry and blur the boundary between surface and subsurface feeding. The dichotomy between microphagous deposit and suspension feeders and macrophagous carnivores, herbivores, and omnivores is further supported by divergent digestive strategies. Deposit feeding appears to be limited largely to worms longer than 1 cm, with juveniles and small worms in general restricted to ingesting highly digestible organic material and larger, rich food items, blurring the macrophage-microphage dichotomy that applies well to larger worms.

Anaerobic digestion of corn stovers for methane production in a novel bionic reactor

To improve the biogas production from corn stovers, a new bionic reactor was designed and constructed. The bionic reactor simulated the rumen digestion of ruminants. The liquid was separated from corn stovers and refluxed into corn stovers again, which simulated the undigested particles separated from completely digested materials and fed back again for further degradation in ruminant stomach. Results showed that the bionic reactor was effective for anaerobic digestion of corn stovers. The liquid amount and its reflux showed an obvious positive correlation with biogas production. The highest biogas production rate was 21.6 ml/gVS-addedd, and the total cumulative biogas production was 256.5 ml/gVS-added. The methane content in biogas ranged from 52.2% to 63.3%. The degradation of corn stovers were greatly enhanced through simulating the animal digestion mechanisms in this bionic reactor.

Transfer of blood urea nitrogen to cecal microbial nitrogen is increased by fructo-oligosaccharide feeding in guinea pigs

The present study was conducted to determine the mechanism by which nitrogen (N) availability is improved by fructo-oligosaccharide (FOS) in guinea pigs. Adult male guinea pigs were fed a commercial pellet diet (50 g/day) with either 5% glucose or 5% FOS for 7 days in individual metabolism cages. After 7 days of feeding the diet, (15) N-urea was administered intravenously 1 h before slaughter under anesthesia. The amount and concentration of total, protein, bacterial, ammonia and urea N and the (15) N atom % excess were measured in blood, liver, gut contents and urine. The (15) N atom % excess of total and protein N, and the amount of total, protein and bacteria N and (15) N in the cecum were significantly increased by the consumption of FOS. Furthermore, the concentration and amount of short-chain fatty acids were significantly increased by the consumption of FOS. In contrast, the amount of urinary (15) N was significantly decreased by the consumption of FOS. These results suggest that consumption of FOS increases transfer of blood urea N into the large intestine for bacterial N synthesis, which is subsequently re-absorbed by cecotrophy, and contributes to the increase of N utilization in guinea pigs.

Lactobacillus acidophilus NCFM affects vitamin E acetate metabolism and intestinal bile acid signature in monocolonized mice

Monocolonization of germ-free (GF) mice enables the study of specific bacterial species in vivo. Lactobacillus acidophilus NCFM(TM) (NCFM) is a probiotic strain; however, many of the mechanisms behind its health-promoting effect remain unknown. Here, we studied the effects of NCFM on the metabolome of jejunum, cecum, and colon of NCFM monocolonized (MC) and GF mice using liquid chromatography coupled to mass-spectrometry (LC-MS). The study adds to existing evidence that NCFM in vivo affects the bile acid signature of mice, in particular by deconjugation. Furthermore, we confirmed that carbohydrate metabolism is affected by NCFM in the mouse intestine as especially the digestion of oligosaccharides (penta- and tetrasaccharides) was increased in MC mice. Additionally, levels of α-tocopherol acetate (vitamin E acetate) were higher in the intestine of GF mice than in MC mice, suggesting that NCFM affects the vitamin E acetate metabolism. NCFM did not digest vitamin E acetate in vitro, suggesting that direct bacterial metabolism was not the cause of the altered metabolome in vivo. Taken together, our results suggest that NCFM affects intestinal carbohydrate metabolism, bile acid metabolism and vitamin E metabolism, although it remains to be investigated whether this effect is unique to NCFM.