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.

Opportunities Lost? Evolutionary Causes and Ecological Consequences of the Absence of Trehalose Digestion in Birds.

AbstractTrehalose is a nonreducing disaccharide that is a primary storage and energy source in prokaryotes, yeasts, fungi, and invertebrates. Vertebrates digest trehalose with the intestinal brush border membrane (BBM) enzyme trehalase. Intestinal trehalase activity is reported to be either very low or absent in several bird species. We assayed trehalase activity in 19 avian species, used proteomic analysis to quantify its abundance in the intestinal BBM, and used analyses of available genomes to detect the presence of the gene that codes for trehalase (Treh). We found no intestinal trehalase activity in birds, trehalase was absent from the proteome of their intestinal BBM, and the gene coding for trehalase was absent in their genomes. Surveys of available transcriptomes support the hypothesis that Treh is absent in birds. The trehalase gene was found in the same conserved syntenic block within the genome of all vertebrates surveyed except birds. Our analysis suggests that Treh was lost in an inversion followed by a reinsertion of a large gene block. This event appears to have taken place after the split between crocodiles and birds and dinosaurs. Birds are unable to digest a common dietary sugar like trehalose because their ancestor lost the trehalase gene. The loss of this gene seems to represent an ecological cost, as insectivorous birds seem to be unable to digest a carbohydrate present in their prey. We also speculate that the paucity of mycophagy in birds is due to the presence of large amounts of this sugar in fungal tissues.

Adaptation of intestinal epithelial hydrolysis and absorption of dietary carbohydrate and protein in mammals and birds.

The small intestine of mammals and birds exhibits fascinating variation across taxa, body size, and life history features such as locomotion and diet. In the intestine's brush border membrane (BBM), hydrolases are more abundant than transporters in both mammals and birds, but there are differences among the groups in abundance of certain hydrolases and possibly in transporters. For example, mammals express two α-glucosidases, sucrase-isomaltase (SI) and maltase glucoamylase (MGAM), whereas songbirds we studied have only SI, and the chicken expresses SI plus another α-glucosidase that functions similarly to MGAM but is not a true ortholog. For intestinal absorption of sugars and amino acids, small fliers rely on a paracellular pathway to a greater extent than do nonflying mammals, which rely more on transporters. Possibly having evolved in fliers as compensation for lower intestinal nominal surface area (NSA), the fliers' reliance on paracellular absorption is supported by their greater villous surface enlargement that leads to more (per cm2 NSA) tight junctions and greater clearance of passively absorbed compounds. To match digestive capacity to nutrient load, a positive relationship is often observed between dietary intake of macronutrients and intestinal activity of the enzymes and transporters of their respective constituents. In enterocytes, rapid, fine-tuned adjustment to high dietary carbohydrate and protein involves rapid, specific correlated increase in activity and abundance of hydrolases and transporters in the BBM and increases in their mRNA.

Rapid and parallel changes in activity and mRNA of intestinal peptidase to match altered dietary protein levels in juvenile house sparrows (Passer domesticus).

Although dietary flexibility in digestive enzyme activity (i.e. reaction rate) is widespread in vertebrates, mechanisms are poorly understood. When laboratory rats are switched to a higher protein diet, the activities of apical intestinal peptidases increase within 15 h, in some cases by rapid increase in enzyme transcription followed by rapid translation and translocation to the intestine's apical, brush-border membrane (BBM). Focusing on aminopeptidase-N (APN), we studied intestinal digestive enzyme flexibility in birds, relying on activity and mRNA data from the same animals. Our model was nestling house sparrows (Passer domesticus), already known to modulate intestinal peptidase activity when switching between lower and higher protein diets. Twenty-four hours after a switch from an adequate, lower protein diet to a higher protein diet, APN activity was increased in both whole intestinal tissue homogenates and in isolated BBM, but not at 12 h post-diet switch. Twenty-four hours after a reverse switch back to the lower protein diet, APN activity was decreased, but not at 12 h post-diet switch. Changes in APN activity in both diet switch experiments were associated with parallel changes in APN mRNA. Although transcriptional changes seem to be an important mechanism underlying dietary modulation of intestinal peptidase in both nestling house sparrows and laboratory rodents, the time course for modulation in nestlings seemed slower (taking approximately twice as long) compared with laboratory rodents. It may be ecologically advantageous if nestlings biochemically restructure their gut in response to a sustained increase in insects and protein intake rather than one or a few lucky insect meals.

Dietary adaptation to high starch involves increased relative abundance of sucrase-isomaltase and its mRNA in nestling house sparrows.

Dietary flexibility in digestive enzyme activity is widespread in vertebrates but mechanisms are poorly understood. When laboratory rats are switched to a higher carbohydrate diet, the activities of the apical intestinal α-glucosidases (AGs) increase within 6-12 h, mainly by rapid increase in enzyme transcription, followed by rapid translation and translocation to the intestine's apical, brush-border membrane (BBM). We performed the first unified study of the overall process in birds, relying on activity, proteomic, and transcriptomic data from the same animals. Our avian model was nestling house sparrows (Passer domesticus), which switch naturally from a low-starch insect diet to a higher starch seed diet and in whom the protein sucrase-isomaltase (SI) is responsible for all maltase and sucrase intestinal activities. Twenty-four hours after the switch to a high-starch diet, SI activity was increased but not at 12 h post diet switch. SI was the only hydrolase increased in the BBM, and its relative abundance and activity were positively correlated. Twenty-four hours after a reverse switch back to the lower starch diet, SI activity was decreased but not at 12 h post diet switch. Parallel changes in SI mRNA relative abundance were associated with the changes in SI activity in both diet-switch experiments, but our data also revealed an apparent diurnal rhythm in SI mRNA. This is the first demonstration that birds may rely on rapid increase in abundance of SI and its mRNA when adjusting to high-starch diet. Although the mechanisms underlying dietary induction of intestinal enzymes seem similar in nestling house sparrows and laboratory rodents, the time course for modulation in nestlings seemed half as fast compared with laboratory rodents. Before undertaking modulation, an opportunistic forager facing limited resources might rely on more extensive or prolonged environmental sampling, because the redesign of the intestine's hydrolytic capacity shortly after just one or a few meals of a new substrate might be a costly mistake.

A Fast and Accurate Method to Identify and Quantify Enzymes in Brush-Border Membranes: In Situ Hydrolysis Followed by Nano LC-MS/MS.

A simple method for the identification of brush-border membrane α-glucosidases is described. The proteins were first solubilized and separated in a gel under native, non-denaturing, conditions. The gel was then incubated in substrate solutions (maltose or sucrose), and the product (glucose) exposed in situ by the oxidation of o-dianisidine, which yields a brown-orange color. Nano-liquid chromatography coupled to mass spectrometry analyses of proteins (nano LC-MS/MS) present in the colored bands excised from the gels, was used to confirm the presence of the enzymes. The stain is inexpensive and the procedure permits testing several substrates in the same gel. Once enzymes are identified, their abundance, relative to that of other proteins in the brush border, can be semi-quantified using nano LC-MS/MS.

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.

Daily expression of sodium-dependent glucose cotransporter-1 protein in jejunum during rat ontogeny.

It is widely known that intestinal capacities such as the enzymatic hydrolysis of carbohydrates, lipids and proteins, and the subsequent absorption of the hydrolyzed products, are evolutionary matched to dietary loads and feeding behaviors. In this study, we demonstrate that the protein expression of apically located sodium-dependent glucose cotransporter-1 (SGLT-1) throughout rat ontogeny is daily adjusted to afford glucose uptake when the load of this metabolically essential monosaccharide in the intestinal lumen is maximum. The jejunal expression of SGLT-1 protein in 14 one-day-old suckling pups was found to increase at dark and early light phase (P < 0.05), when they have a better access to mother milk. In weaning 21-d-old and juvenile 28-d-old rats, the cotransporter expression was high throughout the entire day (P < 0.05). Finally, adult 90-d-old rats showed a well-developed circadian rhythm for SGLT-1 protein (P < 0.05), whose expression increased at late light and dark phase when the highest intestinal glucose load was achieved. To our knowledge, these results are the first reporting the daily profile of SGLT-1 expression during rat early developmental stage and may contribute to understand the biological significance of a well-established molecular capacity to deal with the crucial increase of glucose load in the diet during the weaning process.

Morphological bases for intestinal paracellular absorption in bats and rodents.

Flying mammals present unique intestinal adaptations, such as lower intestinal surface area than nonflying mammals, and they compensate for this with higher paracellular absorption of glucose. There is no consensus about the mechanistic bases for this physiological phenomenon. The surface area of the small intestine is a key determinant of the absorptive capacity by both the transcellular and the paracellular pathways; thus, information about intestinal surface area and micro-anatomical structure can help explain differences among species in absorptive capacity. In order to elucidate a possible mechanism for the high paracellular nutrient absorption in bats, we performed a comparative analysis of intestinal villi architecture and enterocyte size and number in microchiropterans and rodents. We collected data from intestines of six bat species and five rodent species using hematoxylin and eosin staining and histological measurements. For the analysis we added measurements from published studies employing similar methodology, making in total a comparison of nine species each of rodents and bats. Bats presented shorter intestines than rodents. After correction for body size differences, bats had ~41% less nominal surface area (NSA) than rodents. Villous enhancement of surface area (SEF) was ~64% greater in bats than in rodents, mainly because of longer villi and a greater density of villi in bat intestines. Both taxa exhibited similar enterocyte diameter. Bats exceeded rodents by ~103% in enterocyte density per cm2 NSA, but they do not significantly differ in total number of enterocytes per whole animal. In addition, there is a correlation between SEF and clearance per cm2 NSA of L-arabinose, a nonactively transported paracellular probe. We infer that an increased enterocyte density per cm2 NSA corresponds to increased density of tight junctions per cm2 NSA, which provides a partial mechanistic explanation for understanding the high paracellular absorption observed in bats compared to nonflying mammals.

Egg perivitelline fluid of the invasive snail Pomacea canaliculata affects mice gastrointestinal function and morphology.

BACKGROUND: Species beloging to the genus Pomacea (Ampullariidae), often referred as apple snails, are freshwater, amphibious snails native to South, Central and North America. Some species such as P. canaliculata have become a driver of ecosystem changes in wetlands and an important rice and taro pest after its introduction to Asia and other parts of the world. Females deposit colored egg clutches above the waterline, a reproductive strategy that exposes the eggs to harsh conditions and terrestrial predation. However, eggs have no reported predators in their native range, probably because of the acquisition of unparalleled biochemical defenses provided by a set of proteins (perivitellins) that nourish embryos and protect them from predators and abiotic factors. Notably, ingestion of egg perivitelline fluid (PVF) decreases rat growth rate and alters their gastrointestinal morphology. The aim of the study is to determine the effect of apple snail egg PVF on mice gut digestive activity, morphology and nutrient absorption. METHODS: Carbohydrate digestion by intestinal disaccharidases (sucrase-isomaltase and maltase-glucoamylase) was evaluated ex vivo in mice gavaged with 1 or 4 doses of PVF. Changes in gut morphological and absorptive surface were measured. In addition, alteration on nutrient absorption rates, transport pathways and intestinal permeability was evaluated by luminal perfusions of small intestine with radiolabeled L-proline (absorbed by paracellular and transcellular pathways) and L-arabinose (absorbed exclusively by paracellular pathway). RESULTS: Perivitelline fluid affected mice displayed significant morphological changes in the small intestine epithelium inducing the appearance of shorter and wider villi as well as fused villi. This resulted in a diminished absorptive surface, notably in the proximal portion. Likewise, the activity of disaccharidases diminished in the proximal portion of the intestine. Total absorption of L-proline increased in treated mice in a dose-dependent manner. There were no differences neither in the ratio of paracellular-to-transcellular absorption of L-proline nor in gut permeability as revealed by the clearance of L-arabinose. DISCUSSION: Oral administration of apple snail PVF to mice adversely alters gut morphophysiology by reducing the intestinal absorptive surface, affecting enzymes of sugar metabolism and increasing the absorption rate of nutrients without affecting the relative contribution of the absorption pathways or gut permeability. These results further support the role of PVF in passive anti-predator defenses in Pomacea snail eggs that target the digestive system.

Small intestinal epithelial permeability to water-soluble nutrients higher in passerine birds than in rodents.

In the small intestine transcellular and paracellular pathways are implicated in water-soluble nutrient absorption. In small birds the paracellular pathway is quantitatively important while transcellular pathway is much more important in terrestrial mammals. However, there is not a clear understanding of the mechanistic underpinnings of the differences among taxa. This study was aimed to test the hypothesis that paracellular permeability in perfused intestinal segments is higher in passerine birds than rodents. We performed in situ intestinal perfusions on individuals of three species of passerine birds (Passer domesticus, Taeniopygia guttata and Furnarius rufus) and two species of rodents (Mus musculus and Meriones ungiculatus). Using radio-labelled molecules, we measured the uptake of two nutrients absorbed by paracellular and transcellular pathways (L-proline and 3-O-methyl-D-glucose) and one carbohydrate that has no mediated transport (L-arabinose). Birds exhibited ~2 to ~3 times higher L-arabinose clearance per cm2 epithelium than rodents. Moreover, paracellular absorption accounted for proportionally more of 3-O-methyl-D-glucose and L-proline absorption in birds than in rodents. These differences could be explained by differences in intestinal permeability and not by other factors such as increased retention time or higher intestinal nominal surface area. Furthermore, analysis of our results and all other existing data on birds, bats and rodents shows that insectivorous species (one bird, two bats and a rodent) had only 30% of the clearance of L-arabinose of non-insectivorous species. This result may be explained by weaker natural selection for high paracellular permeability in animal- than in plant-consumers. Animal-consumers absorb less sugar and more amino acids, whose smaller molecular size allow them to traverse the paracellular pathway more extensively and faster than glucose.

Intestinal α-glycosidase transcriptional responses during development and diet adjustment in altricial birds.

We describe developmental changes in maltasic activity and its mRNA until adulthood, and in response to an increase in dietary starch. We studied house sparrows (Passer domesticus), which undergo a natural switch from insects to a starch-containing seed diet during development, and zebra finches (Taeniopygia guttata), which have a relatively fixed starchy seed diet during development. In zebra finches, in which maltasic activity increased with age but not with dietary starch, α-glycosidase (AG) mRNA was not affected by either age or dietary starch level. In house sparrow nestlings, in which maltasic activity increased with age and with added starch, AG mRNA was higher when birds were fed a diet with added starch but did not increase with age. These results are consistent with the idea that the apparent programmed developmental increase in maltasic activity is not mainly under transcriptional control of AG mRNA, whereas induction of maltasic activity by increased dietary starch is.

House sparrow biomarkers as lead pollution bioindicators. Evaluation of dose and exposition length on hematological and oxidative stress parameters.

House sparrows (Passer domesticus) have been proposed as a key ecological indicator of urban pollution. Remarkably, we lack knowledge about the physiological effects of lead on this bird species. Therefore, this study was aimed to evaluate the effect of Pb on several physiological parameters in house sparrows exposed to environmental Pb concentrations. In a first experiment, birds were exposed to Pb sub-lethal doses (from 1.3 to 14.0 µg of Pb/g animal/day) during 5 days, which resulted in a dose response increase of blood Pb levels and decrease of blood ALAD activity. However, at the higher doses tested (> 7 µg of Pb/g animal/day) the blood ALAD activity inhibition (~82%) remained constant. Hematocrit and hemoglobin were significantly reduced only at the highest-doses, and the stress indicator, heterophils to lymphocyte (H/L) ratio, did not show apparent changes. In a second experiment, house sparrows were exposed to Pb in drinking water (12.3 ppm) during either 15 or 30 days. Pb concentration used in this study was enough to produce blood lead levels equivalents to those found recently in house sparrows inhabiting urban areas, reduced blood ALAD activity and inversion of the H/L ratio. Decreasing blood ALAD activities were correlated with increasing blood Pb levels. In addition, Pb exposure produced modification in the levels of hepatic antioxidant enzymes, increased GST activity and decreased CAT activity, without lipid peroxidation. In conclusion, our results suggest that blood ALAD activity is a reliable and sensitive biomarker for environmental Pb exposure in house sparrows, additionally chronic exposure produce physiological stress (H/L inversion) and small changes in antioxidant enzyme activity. Finally, this specie could be considered a bioindicator for monitoring the urban Pb contamination.

Gut microbes limit growth in house sparrow nestlings (Passer domesticus) but not through limitations in digestive capacity.

Recent research often lauds the services and beneficial effects of host-associated microbes on animals. However, hosting these microbes may come at a cost. For example, germ-free and antibiotic-treated birds generally grow faster than their conventional counterparts. In the wild, juvenile body size is correlated with survival, so hosting a microbiota may incur a fitness cost. Avian altricial nestlings represent an interesting study system in which to investigate these interactions, given that they exhibit the fastest growth rates among vertebrates, and growth is limited by their digestive capacity. We investigated whether reduction and restructuring of the microbiota by antibiotic treatment would: (i) increase growth and food conversion efficiency in nestling house sparrows (Passer domesticus); (ii) alter aspects of gut anatomy or function (particularly activities of digestive carbohydrases and their regulation in response to dietary change); and (iii) whether there were correlations between relative abundances of microbial taxa, digestive function and nestling growth. Antibiotic treatment significantly increased growth and food conversion efficiency in nestlings. Antibiotics did not alter aspects of gut anatomy that we considered but depressed intestinal maltase activity. There were no significant correlations between abundances of microbial taxa and aspects of host physiology. Overall, we conclude that microbial-induced growth limitation in developing birds is not driven by interactions with digestive capacity. Rather, decreased energetic and material costs of immune function or beneficial effects from microbes enriched under antibiotic treatment may underlie these effects. Understanding the costs and tradeoffs of hosting gut microbial communities represents an avenue of future research.

NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver.

Metabolites present in liver provide important clues regarding the physiological state of an organism. The aim of this work was to evaluate a protocol for high-throughput NMR-based analysis of polar and non-polar metabolites from a small quantity of liver tissue. We extracted the tissue with a methanol/chloroform/water mixture and isolated the polar metabolites from the methanol/water layer and the non-polar metabolites from the chloroform layer. Following drying, we re-solubilized the fractions for analysis with a 600 MHz NMR spectrometer equipped with a 1.7 mm cryogenic probe. In order to evaluate the feasibility of this protocol for metabolomics studies, we analyzed the metabolic profile of livers from house sparrow (Passer domesticus) nestlings raised on two different diets: livers from 10 nestlings raised on a high protein diet (HP) for 4 d and livers from 12 nestlings raised on the HP diet for 3 d and then switched to a high carbohydrate diet (HC) for 1 d. The protocol enabled the detection of 52 polar and nine non-polar metabolites in ¹H NMR spectra of the extracts. We analyzed the lipophilic metabolites by one-way ANOVA to assess statistically significant concentration differences between the two groups. The results of our studies demonstrate that the protocol described here can be exploited for high-throughput screening of small quantities of liver tissue (approx. 100 mg wet mass) obtainable from small animals.

Intestinal digestive enzyme modulation in house sparrow nestlings occurs within 24†h of a change in diet composition.

Nestling house sparrows near fledging age (12 days) were previously found to reversibly modulate the activity of their intestinal digestive enzymes in response to changes in diet composition. However, it is not known how quickly nestlings can adjust to new diets with different substrate compositions, nor is it known how early in life nestlings can modulate their enzyme activity in response to changes in diet. In the present study, 3-day-old nestlings were captured from the wild and fed and switched among contrasting diets - one high in protein and low in carbohydrate and another higher in carbohydrate and with lower, but adequate, protein - in order to determine (1) how quickly house sparrow nestlings could adjust to changes in diet composition, (2) how early in life nestlings could modulate their digestive enzyme activity in response to these changes and (3) which digestive enzymes could be modulated in house sparrow nestlings earlier in life. We found that house sparrow nestlings as young as 3 days post-hatch were capable of modulating their intestinal disaccharidase activity within 24 h of a change in diet composition, and nestlings gained the ability to modulate aminopeptidase-N by 6 or 7 days of age. To our knowledge, this is the first evidence of digestive enzyme modulation completed within 24 h of a change in diet in an avian species and the first study to show intestinal digestive enzyme modulation in response to changes in diet composition in any animal this early in development.

Immune responsiveness to phytohemagglutinin displays species but not sex differences in three anuran species.

Phytohemagglutinin (PHA)-induced skin swelling response is widely used as a rough surrogate of integrative cell-mediated and innate immunity across multiple vertebrate taxa due to its simplification and feasibility. However, little is known whether there are sex and interspecific differences of immune responsiveness to PHA in ectotherms, especially for anurans. Therefore, we studied sex and species differences of PHA response in three anurans, Asiatic toads (Bufo gargarizans), Dark-spotted frogs (Pelophylax nigromaculatus) and Mongolian toads (Pseudepidalea raddei), captured in northern regions of Anhui Province (China). Footpad thickness was measured prior to (0 h) and after (6, 12, 24, 48 and 72 h) a PHA injection and normalized against saline injection in the opposite footpad. Body mass was recorded at the beginning (0 h) and end of each assay (72 h). Results showed effects of PHA assay, sex and taxa on body mass. Relative maximum swelling response (PHAmax) ranged from 18.58-29.75%, 9.77 to 20.56% and 21.97 to 31.78% and its occurrence over time was apparent 10.6-19.72 h , 7.74-14.01 h and 17.39-23.94 h postinjection for Asiatic toads, Dark-spotted frogs and Mongolian toads, respectively. Finally, the magnitude or timing of PHAmax in Dark-spotted frogs was significantly thinner and faster than in Mongolian toads, and Asiatic toads had an in-between value, not different from the other two species. The magnitude of PHAmax was significantly positively correlated with the timing of PHAmax considering individuals altogether, but not when analyzed within species. Our results indicate that male and female anuran species respond similarly to PHA antigen stimulation, but the magnitude and timing of PHAmax is species-specific. Briefly, we provide new evidence for the suitability of PHA assay in non-model anuran species with different body sizes, and exhort the need to further investigate the nature of PHA assay at the hematological and histological levels in order to extend its application in ecoimmunological studies of amphibians.

Modulation of digestive enzyme activities in the avian digestive tract in relation to diet composition and quality.

In nature, birds are faced with variable food sources that may differ in composition (protein vs. carbohydrates) and quality (highly digestible material vs. indigestible fiber). Studies in passerine birds and some commercial poultry demonstrate that the gastrointestinal tract can respond to varying diet composition and quality by changing morphology and/or activities of digestive enzymes. However, studies in additional avian species are warranted to understand generalities of these trends. We first fed juvenile mallards (Anas platyrhynchos), chickens (Gallus gallus), and quails (Coturnix coturnix) on either high-carbohydrate or high-protein diets. For the most part, birds fed the high-carbohydrate diet had higher small intestinal and cecal disaccharidase activities (maltase and sucrase). However, only mallards exhibited higher small intestinal aminopeptidase-N (APN) activities when fed the high-protein diet. These results differ from passerine birds, which largely modulate small intestinal proteases, but not disaccharidases. In another trial, we fed Canada geese (Branta canadensis) diets that varied in both their protein and fiber concentrations for approximately 3.5 months. Birds fed the high-fiber diets had significantly longer small intestines and caeca compared to those fed low-fiber diets. Additionally, geese fed the high-fiber diets exhibited lower mass-specific activities of small intestinal sucrase, and higher activities of APN when summed across the small intestine and ceca. Similar to the avian species above, geese fed the high-protein diets did not exhibit flexibility in their small intestinal APN activities. Overall, these experiments demonstrate that responsiveness of the avian digestive tract to diet composition may have phylogenetic or ecological constraints. Studies on other avian taxa are needed to understand these patterns.

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission.

Animals maintain complex associations with a diverse microbiota living in their guts. Our understanding of the ecology of these associations is extremely limited in reptiles. Here, we report an in-depth study into the microbial ecology of gut communities in three syntopic and viviparous lizard species (two omnivores: Liolaemus parvus and Liolaemus ruibali and an herbivore: Phymaturus williamsi). Using 16S rRNA gene sequencing to inventory various bacterial communities, we elucidate four major findings: (i) closely related lizard species harbour distinct gut bacterial microbiota that remain distinguishable in captivity; a considerable portion of gut bacterial diversity (39.1%) in nature overlap with that found on plant material, (ii) captivity changes bacterial community composition, although host-specific communities are retained, (iii) faecal samples are largely representative of the hindgut bacterial community and thus represent acceptable sources for nondestructive sampling, and (iv) lizards born in captivity and separated from their mothers within 24 h shared 34.3% of their gut bacterial diversity with their mothers, suggestive of maternal or environmental transmission. Each of these findings represents the first time such a topic has been investigated in lizard hosts. Taken together, our findings provide a foundation for comparative analyses of the faecal and gastrointestinal microbiota of reptile hosts.

Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard.

While herbivory is a common feeding strategy in a number of vertebrate classes, less than 4% of squamate reptiles feed primarily on plant material. It has been hypothesized that physiological or microbial limitations may constrain the evolution of herbivory in lizards. Herbivorous lizards exhibit adaptations in digestive morphology and function that allow them to better assimilate plant material. However, it is unknown whether these traits are fixed or perhaps phenotypically flexible as a result of diet. Here, we maintained a naturally omnivorous lizard, Liolaemus ruibali, on a mixed diet of 50% insects and 50% plant material, or a plant-rich diet of 90% plant material. We compared parameters of digestive performance, gut morphology and function, and gut microbial community structure between the two groups. We found that lizards fed the plant-rich diet maintained nitrogen balance and exhibited low minimum nitrogen requirements. Additionally, lizards fed the plant-rich diet exhibited significantly longer small intestines and larger hindguts, demonstrating that gut morphology is phenotypically flexible. Lizards fed the plant-rich diet harbored small intestinal communities that were more diverse and enriched in Melainabacteria and Oscillospira compared with mixed diet-fed lizards. Additionally, the relative abundance of sulfate-reducing bacteria in the small intestine significantly correlated with whole-animal fiber digestibility. Thus, we suggest that physiological and microbial limitations do not sensu stricto constrain the evolution of herbivory in lizards. Rather, ecological context and fitness consequences may be more important in driving the evolution of this feeding strategy.