Mammalian intestinal allometry, phylogeny, trophic level and climate

Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi)

The composition of mammalian gut microbiomes is highly conserved within species, yet the mechanisms by which microbiome composition is transmitted and maintained within lineages of wild animals remain unclear. Mutually compatible hypotheses exist, including that microbiome fidelity results from inherited dietary habits, shared environmental exposure, morphophysiological filtering and/or maternal effects. Interspecific hybrids are a promising system in which to interrogate the determinants of microbiome composition because hybrids can decouple traits and processes that are otherwise co-inherited in their parent species. We used a population of free-living hybrid zebras (Equus quagga × grevyi) in Kenya to evaluate the roles of these four mechanisms in regulating microbiome composition. We analysed faecal DNA for both the trnL-P6 and the 16S rRNA V4 region to characterize the diets and microbiomes of the hybrid zebra and of their parent species, plains zebra (E. quagga) and Grevy's zebra (E. grevyi). We found that both diet and microbiome composition clustered by species, and that hybrid diets and microbiomes were largely nested within those of the maternal species, plains zebra. Hybrid microbiomes were less variable than those of either parent species where they co-occurred. Diet and microbiome composition were strongly correlated, although the strength of this correlation varied between species. These patterns are most consistent with the maternal-effects hypothesis, somewhat consistent with the diet hypothesis, and largely inconsistent with the environmental-sourcing and morphophysiological-filtering hypotheses. Maternal transmittance likely operates in conjunction with inherited feeding habits to conserve microbiome composition within species.

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.

Vascularization of the gastrointestinal tract of the bottlenose dolphin (Tursiops truncatus, Montagu 1821)

Odontocetes primarily rely on fish, cephalopods, and crustaceans as their main source of nutrition. In the digestive system, their polygastric complex exhibits similarities to that of their closest terrestrial relatives such as cows, sheep, and giraffes, while the entero-colic tract shares similarities with terrestrial carnivores. The morphology, caliber, and structure of the odontocete intestine are relatively constant, and, since there is no caecum, a distinction between the small and large intestine and their respective subdivisions is difficult. To address this issue, we used the intestinal vascularization pattern, specifically the course and branching of the celiac artery (CA) and the cranial and caudal mesenteric arteries (CrMA and CdMA). A series of pictures and dissections of 10 bottlenose dolphins (Tursiops truncatus) were analyzed. Additionally, we performed a cast by injecting colored polyurethane foam in both arteries and veins to measure the caliber of the arteries and clarify their monopodial or dichotomous branching. Our results showed the presence of multiple duodenal arteries (DAs) detaching from the CA. The CrMA gave origin to multiple jejunal arteries, an ileocolic artery (ICA), and, in six cases, a CdMA. In four specimens, the CdMA directly originated from the abdominal aorta. The ICA gave rise to the mesenteric ileal branches (MIB) and mesenteric anti-ileal branches and the right colic arteries (RCA) and the middle colic arteries. From the CdMA originated the left colic and cranial rectal arteries (LCA and CrRA). The measurements revealed a mixed monopodial and dichotomous branching scheme. The analysis of the arteries and their branching gave us an instrument, based on comparative anatomy, to distinguish between the different intestinal compartments. We used the midpoint of anastomoses between MIB and RCA to indicate the border between the small and the large intestine, and the midpoint of anastomoses between LCA and CrRA, to tell the colon from the rectum. This pattern suggested an elongation of the duodenum and a shortening of the colic tract that is still present in this species. These findings might be related to the crucial need to possess a long duodenal tract to digest prey ingested whole without chewing. A short aboral part is also functional to avoid gas-producing colic fermentation. The rare origin of the CdMA on the CrMA might instead be a consequence of the cranial thrust of the abdominopelvic organs related to the loss of the pelvic girdle that occurred during the evolution of cetaceans.

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'.

Campylobacter jejuni benefits from the bile salt deoxycholate under low-oxygen condition in a PldA dependent manner

Enteric bacteria need to adapt to endure the antibacterial activities of bile salts in the gut. Phospholipase A (PldA) is a key enzyme in the maintenance of bacterial membrane homeostasis. Bacteria respond to stress by modulating their membrane composition. Campylobacter jejuni is the most common cause of human worldwide. However, the mechanism by which C. jejuni adapts and survives in the gut environment is not fully understood. In this study, we investigated the roles of PldA, bile salt sodium deoxycholate (DOC), and oxygen availability in C. jejuni biology, mimicking an in vivo situation. Growth curves were used to determine the adaptation of C. jejuni to bile salts. RNA-seq and functional assays were employed to investigate the PldA-dependent and DOC-induced changes in gene expression that influence bacterial physiology. Survival studies were performed to address oxidative stress defense in C. jejuni. Here, we discovered that PldA of C. jejuni is required for optimal growth in the presence of bile salt DOC. Under high oxygen conditions, DOC is toxic to C. jejuni, but under low oxygen conditions, as is present in the lumen of the gut, C. jejuni benefits from DOC. C. jejuni PldA seems to enable the use of iron needed for optimal growth in the presence of DOC but makes the bacterium more vulnerable to oxidative stress. In conclusion, DOC stimulates C. jejuni growth under low oxygen conditions and alters colony morphology in a PldA-dependent manner. C. jejuni benefits from DOC by upregulating iron metabolism in a PldA-dependent manner.

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.

No news from old drawings? Stomach anatomy in muroid rodents in relation to body size and ecology

Muroid rodents mostly have a complex stomach: one part is lined with a cornified (nonglandular) epithelium, referred to as a "forestomach", whereas the rest is lined with glandular epithelium. Numerous functions for the forestomach have been proposed. We collated a catalog of anatomical depictions of the stomach of 174 muroid species from which the respective nonglandular and glandular areas could be digitally measured, yielding a "stomach ratio" (nonglandular:glandular area) as a scale-independent variable. Stomach ratios ranged from 0.13 to 20.15, and the coefficient of intraspecific variation if more than one picture was available for a species averaged at 29.7% (±21.5). We tested relationships of the ratio with body mass and various anatomical and ecological variables, including diet. There was a consistent phylogenetic signal, suggesting that closely related species share a similar anatomy. Apart from classifying stomachs into hemiglandular and discoglandular, no anatomical or ecological measure showed a consistent relationship to the stomach ratio. In particular, irrespective of statistical method or the source of dietary information, dietary proxies did not significantly correlate with the stomach ratio, except for a trend towards significance for invertivory (insectivory). Yet, even this relationship was not convincing: whereas highly insectivorous species had high but no low stomach ratios, herbivorous species had both low and high stomach ratios. Thus, the statistical effect is not due to a systematic increase in the relative forestomach size with invertivory. The most plausible hypotheses so far associate the muroid forestomach and its microbiome with a generic protective role against microbial or fungal toxins and diseases, without evident correlates of a peculiar need for this function under specific ecological conditions. Yet, this function remains to be confirmed. While providing a catalog of published depictions and hypotheses, this study highlights that the function of the muroid rodent forestomach remains enigmatic to date.

Comparative digestive morphology and physiology of five species of Peromyscus under controlled environment and diet

Digestive morphology and physiology differ across animal species, with many comparative studies uncovering relationships between animal ecology or diet, and the morphology and physiology of the gastrointestinal tract. However, many of these studies compare wild-caught animals feeding on uncontrolled diets and compare broadly related taxa. Thus, few studies have disentangled the phenotypic consequences of genetics from those potentially caused by the environment, especially across closely related species that occupy similar ecological niches. Here, we examined differences in digestive morphology and physiology of five closely related species of Peromyscus mice that were captive bred under identical environmental conditions and identical diets for multiple generations. Using phylogenetic generalized least squares (PGLS) of species means to control for body size, we identified a phylogenetic signal in the mass of the foregut and length of the small intestine across species. As proportions of total gut mass, we identified phylogenetic signals in relative foregut and small intestine masses, indicating that the sizes of these structures are more similar among closely related species. Finally, we detected differences in activities of the protease aminopeptidase-N enzyme across species. Overall, we demonstrate fine-scale differences in digestive morphology and physiology among closely related species. Our results suggest that Peromyscus could provide a system for future studies to explore the interplay between natural history, morphology, and physiology (e.g. ecomorphology and ecophysiology), and to investigate the genetic architecture that underlies gut anatomy.

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.

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.

Mammalian intestinal allometry, phylogeny, trophic level and climate

An often-stated ecomorphological assumption that has the status of 'textbook knowledge' is that the dimensions of the digestive tract correlate with diet, where herbivores-consuming diets of lower digestibility-have longer intestinal tracts than faunivores-consuming diets of higher digestibility. However, statistical approaches have so far failed to demonstrate this link. Here, we collated data on the length of intestinal sections and body mass of 519 mammal species, and test for various relationships with trophic, climatic and other biological characteristics. All models showed a strong phylogenetic signal. Scaling relationships with body mass showed positive allometry at exponents greater than 0.33, except for the caecum, which is particularly large in smaller species. Body mass was more tightly linked to small intestine than to large intestine length. Adding a diet proxy to the relationships increased model fit for all intestinal sections, except for the small intestine when accounting for phylogeny. Thus, the diet has a main effect on the components of the large intestine, with longer measures in herbivores. Additionally, measures of habitat aridity had a positive relationship with large intestine length. The small intestine was longer in species from colder habitats at higher latitudes, possibly facilitating the processing of peak intake rates during the growing season. This study corroborates intuitive expectations on digestive tract anatomy, while the dependence of significant results on large sample sizes and inclusion of specific taxonomic groups indicates that the relationships cannot be considered fixed biological laws.