A quantitative study of the morphological development and bacterial colonisation of the gut of the tammar wallaby Macropus eugenii eugenii and brushtail possum Trichosurus vulpecula during in-pouch development

Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development

The acquisition and maturation of the gastrointestinal microbiome is a crucial aspect of mammalian development, particularly for specialist herbivores such as the koala (Phascolarctos cinereus). Joey koalas are thought to be inoculated with microorganisms by feeding on specialized maternal faeces (pap). We found that compared to faeces, pap has higher microbial density, higher microbial evenness and a higher proportion of rare taxa, which may facilitate the establishment of those taxa in joey koalas. We show that the microbiomes of captive joey koalas were on average more similar to those of their mothers than to other koalas, indicating strong maternal inheritance of the faecal microbiome, which can lead to intergenerational gut dysbiosis when the mother is ill. Directly after pap feeding, the joey koalas' microbiomes were enriched for milk-associated bacteria including Bacteroides fragilis, suggesting a conserved role for this species across mammalian taxa. The joeys' microbiomes then changed slowly over 5 months to resemble those of adults by 1 year of age. The relative abundance of fibrolytic bacteria and genes involved in the degradation of plant cell walls also increased in the infants over this time, likely in response to an increased proportion of Eucalyptus leaves in their diets.

Ontogenetic scaling of the gastrointestinal tract of a marsupial foregut fermenter, the western grey kangaroo Macropus fuliginosus melanops

As an animal grows, the relative sizes of their organs may grow proportionately or disproportionately, depending on ontogenetic changes in function. If organ growth is proportional (isometric), then the exponent of the scaling equation is 1.0. Relative decreases or increases in size result in exponents less than 1 (hypoallometric) or greater than 1 (hyperallometric). Thus, the empirical exponent can indicate potential changes in function. The entire gastrointestinal tract (GIT) of the foregut-fermenting western grey kangaroo Macropus fuliginosus melanops exhibited biphasic allometry across five orders of magnitude body mass (M_b; 52.0 g-70.5 kg). Prior to weaning at around 12 kg M_b, the entire empty GIT mass scaled with hyperallometry (M_b^1.13), shifting to hypoallometry (M_b^0.80) post-weaning. In addition, there were varying patterns of hyper-, hypo-, and isometric scaling for select GIT organs, with several displaying phase shifts associated with major life-history events, specifically around exit from the maternal pouch and around weaning. Mass of the kangaroo forestomach, the main fermentation site, scaled with hyperallometry (M_b^1.16) before the stage of increased vegetation intake, and possibly after this stage (M_b^1.12; P = 0.07), accompanied by a higher scaling factor (elevation of the curve) probably associated with more muscle for processing fibrous vegetation. The acid hindstomach mass showed hyperallometry (M_b^1.15) before weaning, but hypoallometry (M_b ^0.58) post-weaning, presumably associated with decreasing intake of milk. Small intestine mass and length each scaled isometrically throughout ontogeny, with no discernible breakpoints at any life-history stage. The caecum and colon mass were steeply hyperallometric early in-pouch life (M_b^1.59-1.66), when the young were ectothermic, hairless, and supported solely by milk. After around 295 g M_b, caecum mass remained hyperallometric (M_b^1.14), possibly supporting its early development as a nidus for microbial populations to provide for secondary fermentation in this organ after the young transition from milk to vegetation.

Metagenomic analysis of the gut microbiota of the Timber Rattlesnake, Crotalus horridus

Snakes are capable of surviving long periods without food. In this study we characterized the microbiota of a Timber Rattlesnake (Crotalus horridus), devoid of digesta, living in the wild. Pyrosequencing-based metagenomics were used to analyze phylogenetic and metabolic profiles with the aid of the MG-RAST server. Pyrosequencing of samples taken from the stomach, small intestine and colon yielded 691696, 957756 and 700419 high quality sequence reads. Taxonomic analysis of metagenomic reads indicated Eukarya was the most predominant domain, followed by bacteria and then viruses, for all three tissues. The most predominant phylum in the domain Bacteria was Proteobacteria for the tissues examined. Functional classifications by the subsystem database showed cluster-based subsystems were most predominant (10-15 %). Almost equally predominant (10-13 %) was carbohydrate metabolism. To identify bacteria in the colon at a finer taxonomic resolution, a 16S rRNA gene clone library was created. Proteobacteria was again found to be the most predominant phylum. The present study provides a baseline for understanding the microbial ecology of snakes living in the wild.

Post-natal growth of the gastrointestinal tract of the Siberian hamster: morphometric analysis

Post-natal growth of the gastrointestinal tract of the Siberian hamster was studied in newborn and 3-, 7-, 14-, 21-, 42- and 90-day-old animals. Morphometric measurements and calculations were carried out: length and internal surface of gastrointestinal tract segments, size (height, width, surface) and density of villi as well as allometric growth rate of the length and internal surface of the segments with respect to the body mass. The fastest growth rate of the gastrointestinal tract segments was noticed during the first 3 days of the post-natal life. Nevertheless, significant regional differences in their growth rate were found. The increase in the length and internal surface of the large intestine was fastest, while the smallest increase was observed in the oesophagus. All segments of the gastrointestinal tract except oesophagus exhibited a positive allometric relationship to the body mass from birth till final weaning, whereas during the post-weaning period, the increase was isometric. Thus, at birth, the gastrointestinal tract segments were relatively smaller compared with those observed in adults, but then, the gastrointestinal tract grew faster than the rest of the body and reached its adult proportions just before the transition to solid food. Most probably, reaching the adult structure of the gastrointestinal tract before the final weaning is an essential condition for the proper growth of an organism after the weaning.

Developmental changes in the electroencephalogram and responses to a noxious stimulus in anaesthetized tammar wallaby joeys (Macropus eugenii eugenii)

The tammar wallaby joey is born extremely immature and most of its neurological development occurs in the maternal pouch. It is not known at what in-pouch age functions such as conscious sensory perception commence. We determined the electroencephalographic (EEG) responses to noxious stimulation in lightly anaesthetized tammar wallaby joeys. Baseline median (F50) and spectral edge (F95) frequencies, total power (Ptot) and frequency spectra between 1 and 30 Hz of the EEG power spectrum were determined. Joeys aged less than 127 days showed little or no EEG activity. Prolonged periods of spontaneous EEG activity were present by 142 days. This activity increased, as did the power in all frequencies, while the duration of any intervening isoelectric periods decreased with increasing in-pouch age. EEG responses to a noxious stimulus (toe clamping) changed with increasing in-pouch age as there was no response from joeys aged 94-127 days (no EEG), a minimal decrease in the F50 in those aged between 142 and 181 days (P = 0.052) and a greater decrease in the F50 in those aged between 187 and 261 days (P < 0.001). The pattern of these changes, which presumably reflects anatomical and functional maturation of the cerebral cortex, is similar to, but develops more slowly than, that reported in the rat. The opening of the eyes and development of the pelage are discussed as markers of when brain development may be sufficient for joeys to consciously perceive noxious sensations including pain.

An observational study of the microbiome of the maternal pouch and saliva of the tammar wallaby, Macropus eugenii, and of the gastrointestinal tract of the pouch young

Marsupial mammals, born in an extremely atricial state with no functional immune system, offer a unique opportunity to investigate both the developing microbiome and its relationship to that of the mother and the potential influence of this microbiome upon the development of the immune system. In this study we used a well-established marsupial model animal, Macropus eugenii, the tammar wallaby, to document the microbiome of three related sites: the maternal pouch and saliva, and the gastrointestinal tract (GIT) of the young animal. We used molecular-based methods, targeting the 16S rDNA gene to determine the bacterial diversity at these study sites. In the maternal pouch, 41 unique phylotypes, predominantly belonging to the phylum Actinobacteria, were detected, while in the saliva, 48 unique phylotypes were found that predominantly belonged to the phylum Proteobacteria. The GIT of the pouch young had a complex microbiome of 53 unique phylotypes, even though the pouch young were still permanently attached to the teat and had only been exposed to the external environment for a few minutes immediately after birth while making their way from the birth canal to the maternal pouch. Of these 53 phylotypes, only nine were detected at maternal sites. Overall, the majority of bacteria isolated were novel species (<97 % identity to known 16S rDNA sequences), and each study site (i.e. maternal pouch and saliva, and the GIT of the pouch young) possessed its own unique microbiome.

The microbiome of the cloacal openings of the urogenital and anal tracts of the tammar wallaby, Macropus eugenii

The bacterial diversity of the openings of the urogenital and anal tracts of the adult female tammar wallaby, Macropus eugenii, was determined in order to ascertain whether the physical proximity of the openings of these tracts within the cloaca affected the two populations of bacteria. Terminal restriction fragment length polymorphism (T-RFLP) analyses of 42 wallabies identified 81 different terminal fragments, indicative of diverse and complex microbiomes at these anatomical locations. Subsequent amplified rDNA restriction analysis (ARDRA) identified 72 phylotypes from the urogenital tract and 50 from the anal tract. Twenty-two of these phylotypes were common to both tracts. Phylogenetic analysis of sequenced 16S rDNA showed that 83 % of the phylotypes were unidentified species based on the premise that any sequence possessing <97 % homology to a known bacterial species or phylotype was novel. Thus, despite the close proximity of the openings of the urogenital and anal tracts within the cloaca, the two sites retained a diverse range of distinct bacteria, with only a small percentage of overlapping species.

Changes in tissue nucleic acid content and mucosal morphology during intestinal development in pouch young of the tammar wallaby (Macropus eugenii eugenii)

DNA and RNA content and the timing of development of various histological features in the small and large intestine of in-pouch tammar wallabies (Macropus eugenii eugenii) of various ages were measured. A significant decline in gut tissue DNA concentrations and increase in the RNA/DNA ratios over 300 days postpartum indicated that the early postnatal increase in gut tissue mass resulted largely from hypertrophy. Mean duodenal and ileal villus height and crypt depth were significantly greater for in-pouch young aged >100 days compared with those <100 days and were significantly greater in the duodenum than in the ileum. Goblet cells appeared more slowly during development and were fewer in number in the duodenal than in the colonic mucosa. The numbers of mucin-secreting duodenal goblet cells were greater in pouch young aged >100 days than in young aged <100 days. The colonic mucosa exhibited no villi or villus-like folds. Colonic crypt depth increased uniformly with age.