Microflora of the pouch of the koala (Phascolarctos cinereus)

Marsupial immune protection is shaped by enhancer sharing and gene cluster duplication of cathelicidin antimicrobial peptides

Marsupial neonates are born with immature immune systems, making them vulnerable to pathogens. While neonates receive maternal protection, they can also independently combat pathogens, though the mechanisms remain unknown. Using the sugar glider (Petaurus breviceps) as a model, we investigated immunological defense strategies of marsupial neonates. Cathelicidins, a family of antimicrobial peptides expanded in the genomes of marsupials, are highly expressed in developing neutrophils. Sugar glider cathelicidins reside in two genomic clusters and their coordinated expression is achieved by enhancer sharing within clusters and long-range physical interactions between clusters. These cathelicidins modulate immune responses and have potent antimicrobial effects, sufficient to provide protection in a mouse model of sepsis. Lastly, cathelicidins have a complex evolutionary history, where marsupials and monotremes are the only tetrapods that retained two cathelicidin clusters. Thus, cathelicidins are critical mediators of marsupial immunity, and their evolution reflects the life history-specific immunological needs of these animals.

Characterising the Tasmanian devil (Sarcophilus harrisii) pouch microbiome in lactating and non-lactating females

Wildlife harbour a diverse range of microorganisms that affect their health and development. Marsupials are born immunologically naïve and physiologically underdeveloped, with primary development occurring inside a pouch. Secretion of immunological compounds and antimicrobial peptides in the epithelial lining of the female's pouch, pouch young skin, and through the milk, are thought to boost the neonate's immune system and potentially alter the pouch skin microbiome. Here, using 16S rRNA amplicon sequencing, we characterised the Tasmanian devil pouch skin microbiome from 25 lactating and 30 non-lactating wild females to describe and compare across these reproductive stages. We found that the lactating pouch skin microbiome had significantly lower amplicon sequence variant richness and diversity than non-lactating pouches, however there was no overall dissimilarity in community structure between lactating and non-lactating pouches. The top five phyla were found to be consistent between both reproductive stages, with over 85% of the microbiome being comprised of Firmicutes, Proteobacteria, Fusobacteriota, Actinobacteriota, and Bacteroidota. The most abundant taxa remained consistent across all taxonomic ranks between lactating and non-lactating pouch types. This suggests that any potential immunological compounds or antimicrobial peptide secretions did not significantly influence the main community members. Of the more than 16,000 total identified amplicon sequence variants, 25 were recognised as differentially abundant between lactating and non-lactating pouches. It is proposed that the secretion of antimicrobial peptides in the pouch act to modulate these microbial communities. This study identifies candidate bacterial clades on which to test the activity of Tasmanian devil antimicrobial peptides and their role in pouch young protection, which in turn may lead to future therapeutic development for human diseases.

Characterisation of the koala (Phascolarctos cinereus) pouch microbiota in a captive population reveals a dysbiotic compositional profile associated with neonatal mortality

BACKGROUND

Captive koala breeding programmes are essential for long-term species management. However, breeding efficacy is frequently impacted by high neonatal mortality rates in otherwise healthy females. Loss of pouch young typically occurs during early lactation without prior complications during parturition and is often attributed to bacterial infection. While these infections are thought to originate from the maternal pouch, little is known about the microbial composition of koala pouches. As such, we characterised the koala pouch microbiome across the reproductive cycle and identified bacteria associated with mortality in a cohort of 39 captive animals housed at two facilities.

RESULTS

Using 16S rRNA gene amplicon sequencing, we observed significant changes in pouch bacterial composition and diversity between reproductive time points, with the lowest diversity observed following parturition (Shannon entropy - 2.46). Of the 39 koalas initially sampled, 17 were successfully bred, after which seven animals lost pouch young (overall mortality rate - 41.18%). Compared to successful breeder pouches, which were largely dominated by Muribaculaceae (phylum - Bacteroidetes), unsuccessful breeder pouches exhibited persistent Enterobacteriaceae (phylum - Proteobacteria) dominance from early lactation until mortality occurred. We identified two species, Pluralibacter gergoviae and Klebsiella pneumoniae, which were associated with poor reproductive outcomes. In vitro antibiotic susceptibility testing identified resistance in both isolates to several antibiotics commonly used in koalas, with the former being multidrug resistant.

CONCLUSIONS

This study represents the first cultivation-independent characterisation of the koala pouch microbiota, and the first such investigation in marsupials associated with reproductive outcomes. Overall, our findings provide evidence that overgrowth of pathogenic organisms in the pouch during early development is associated with neonatal mortality in captive koalas. Our identification of previously unreported, multidrug resistant P. gergoviae strains linked to mortality also underscores the need for improved screening and monitoring procedures aimed at minimising neonatal mortality in future. Video Abstract.

Koala cathelicidin PhciCath5 has antimicrobial activity, including against Chlamydia pecorum

Devastating fires in Australia over 2019-20 decimated native fauna and flora, including koalas. The resulting population bottleneck, combined with significant loss of habitat, increases the vulnerability of remaining koala populations to threats which include disease. Chlamydia is one disease which causes significant morbidity and mortality in koalas. The predominant pathogenic species, Chlamydia pecorum, causes severe ocular, urogenital and reproductive tract disease. In marsupials, including the koala, gene expansions of an antimicrobial peptide family known as cathelicidins have enabled protection of immunologically naïve pouch young during early development. We propose that koala cathelicidins are active against Chlamydia and other bacteria and fungi. Here we describe ten koala cathelicidins, five of which contained full length coding sequences that were widely expressed in tissues throughout the body. Focusing on these five, we investigate their antimicrobial activity against two koala C. pecorum isolates from distinct serovars; MarsBar and IPTaLE, as well as other bacteria and fungi. One cathelicidin, PhciCath5, inactivated C. pecorum IPTaLE and MarsBar elementary bodies and significantly reduced the number of inclusions compared to the control (p<0.0001). Despite evidence of cathelicidin expression within tissues known to be infected by Chlamydia, natural PhciCath5 concentrations may be inadequate in vivo to prevent or control C. pecorum infections in koalas. PhciCath5 also displayed antimicrobial activity against fungi and Gram negative and positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Electrostatic interactions likely drive PhciCath5 adherence to the pathogen cell membrane, followed by membrane permeabilisation leading to cell death. Activity against E. coli was reduced in the presence of 10% serum and 20% whole blood. Future modification of the PhciCath5 peptide to enhance activity, including in the presence of serum/blood, may provide a novel solution to Chlamydia infection in koalas and other species.

Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Background

Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages.

Results

Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches.

Conclusions

This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00074-8.

Blood constituents of free-ranging eastern grey kangaroos (Macropus giganteus)

Baseline haematology, blood chemistry and acute phase protein parameters have not previously been published for free-ranging eastern grey kangaroos (Macropus giganteus). Eight eastern grey kangaroos, including three adult males, three adult females and two subadult males from two different populations, were examined. Assays assessed the antibacterial activity of kangaroo serum against one Gram-positive and three Gram-negative bacteria. The kangaroo serum had a strong antibacterial response to Klebsiella pneumoniae, and moderate responses to Escherichia coli and Staphylococcus aureus. The presence and level of acute phase proteins, haptoglobin and serum amyloid A in kangaroos was investigated. Haptoglobin and serum amyloid A were present in kangaroo serum, but only haptoglobin was elevated in a kangaroo with capture myopathy and necrotic wounds. The findings of this study provide preliminary data on health parameters of free-ranging eastern grey kangaroos. These parameters can be used to assist in assessing health in free-ranging populations.

Antimicrobial Protection of Marsupial Pouch Young

Marsupials diverged from eutherian mammals about 148 million years ago and represent a unique lineage of mammals with distinctive morphological and reproductive characteristics. Marsupials have significantly shorter gestation periods than eutherians. Pregnancy typically ranges from 15 to 35 days, with young being born at a very early developmental stage and lacking differentiated lymphoid tissues and mature effector cells. Recent microbiome studies of the marsupial pouch revealed that marsupial young can face intense microbial challenges after birth, as the pouch contains a broad range of Gram-positive and Gram-negative bacteria. Antimicrobials are believed to play a significant role in the immune protection of marsupial newborns during their pouch life. The skin of the post-reproductive pouch secretes antimicrobial lysozyme and dermcidin, which may contribute to the decreased density of certain bacteria in the pouch. A range of antimicrobial agents, such as immunoglobulins, lysozyme, transferrin, and cathelicidins, have been identified in marsupial milk. Antimicrobial assays have revealed that marsupial cathelicidins have broad-spectrum activity against a variety of bacteria and fungi, including several multi-drug resistant strains. In this article, we will review the action mechanisms of these antimicrobial compounds and discuss how they protect marsupial newborns from potentially pathogenic bacteria inside the pouch. We will also discuss the potential of marsupial antimicrobial compounds as a source of novel antibiotics.

Glucose modulates Drosophila longevity and immunity independent of the microbiota

The acquisition of nutrients is essential for maintenance of metabolic processes in all organisms. Nutritional imbalance contributes to myriad metabolic disorders that include malnutrition, diabetes and even cancer. Recently, the importance of macronutrient ratio of food has emerged as a critical factor to determine health outcomes. Here we show that individual modifications to a completely defined diet markedly impact multiple aspects of organism wellbeing in Drosophila melanogaster. Through a longitudinal survey of several diets we demonstrate that increased levels of dietary glucose significantly improve longevity and immunity in adult Drosophila. Our metagenomic studies show that relative macronutrient levels not only influence the host, but also have a profound impact on microbiota composition. However, we found that elevated dietary glucose extended the lifespan of adult flies even when raised in a germ-free environment. Furthermore, when challenged with a chronic enteric infection, flies fed a diet with added glucose had increased survival times even in the absence of an intact microbiota. Thus, in contrast to known links between the microbiota and animal health, our findings uncover a novel microbiota-independent response to diet that impacts host wellbeing. As dietary responses are highly conserved in animals, we believe our results offer a general understanding of the association between glucose metabolism and animal health.

A review of complementary mechanisms which protect the developing marsupial pouch young

Marsupials are born without a functioning adaptive immune system, into a non-sterile environment where they continue to develop. This review examines the extent of exposure of pouch young to microorganisms and describes the protective mechanisms that are complementary to adaptive immunity in the developing young. Complementary protective mechanisms include the role of the innate immune system and maternal protection strategies, such as immune compounds in milk, prenatal transfer of immunoglobulins, antimicrobial compounds secreted in the pouch, and chemical or mechanical cleaning of the pouch and pouch young.

Tammar wallaby mammary cathelicidins are differentially expressed during lactation and exhibit antimicrobial and cell proliferative activity

Cathelicidins secreted in milk may be central to autocrine feedback in the mammary gland for optimal development in addition to conferring innate immunity to both the mammary gland and the neonate. This study exploits the unique reproductive strategy of the tammar wallaby (Macropus eugenii) model to analyse differential splicing of cathelicidin genes and to evaluate the bactericidal activity and effect of the protein on mammary epithelial cell proliferation. Two linear peptides, Con73 and Con218, derived from the heterogeneous carboxyl end of cathelicidin transcripts, MaeuCath1 and MaeuCath7 respectively, were evaluated for antimicrobial activity. Both Con73 and Con218 significantly inhibited the growth of Staphylococcus aureus, Pseudomonas aureginosa, Enterococcus faecalis and Salmonella enterica. In addition both MaeuCath1 and MaeuCath7 stimulated proliferation of primary tammar wallaby mammary epithelial cells (WallMEC). Lactation-phase specific alternate spliced transcripts were determined for MaeuCath1 showing utilisation of both antimicrobial and proliferative functions are required by the mammary gland and the suckled young. The study has shown for the first time that temporal regulation of milk cathelicidins may be crucial in antimicrobial protection of the mammary gland and suckled young and mammary cell proliferation.

A proteomic approach to analysis of antimicrobial activity in marsupial pouch secretions

We have documented the antimicrobial activity of pouch secretions of the tammar wallaby, Macropus eugenii, over the period leading up to birth and after birth of the young animal. This activity was greatest against the Gram-negative Escherichia coli and highest at the time of birth. Fractionation of the pouch secretions showed that activity at different times over the reproductive periods was associated with different molecular-weight (MW) components, with compounds in the range up to 50 kDa active immediately prior to and at the time of birth. Proteomic analysis using 1 and 2DE PAGE and LC-MS/MS identified the major components of the pouch secretions at these times, at a range of pI's and MWs. The majority of high-confidence identifications, at a wide range of pI's and MW, were beta-lactoglobulin, a known component of marsupial milk. We subsequently conducted a proteomic analysis of mammary gland secretions and digest products from the gut of the young animal, using 2DE PAGE and MALDI MS/MS, to confirm its source and compare it with the observed MW and pI's of beta-lactoglobulin. Although we did not directly identify an effector molecule responsible for antimicrobial activity, these results lead us to propose that beta-lactoglobulin plays a role in the protection of the young marsupial, a role previously thought to be primarily due to specific secretions from the epithelial surface of the pouch.

Characterisation of and immunity to the aerobic bacteria found in the pouch of the brushtail possum Trichosurus vulpecula

The bacterial composition of the brustail possum (Trichosurus vulpecula) pouch was characterized throughout the reproductive cycle using brushtails from an Australian captive breeding colony (45 swabs) and a wild population in New Zealand (26 swabs). Gram-positive coccal species predominate throughout the reproductive cycle. Enteric Gram-negative rods, particularly Escherichia coli, were most prevalent when a pouch young was present and was most likely the result of faecal contamination from the pouch young. As culturing is only able to detect a proportion of bacteria present in a particular environment, molecular 16S rDNA sequencing was carried out on DNA extracted from a pouch wash of a female carrying a pouch young to gain a more accurate assessment of the pouch microflora. This approach identified approximately five times the number of bacterial species when compared to culture results. The majority detected were Gram negative rods or most closely related to Gram-negative rods species. Brushtails are immunologically immature at birth yet survive in a pouch colonised with potentially pathogenic bacteria. A haemagglutination assay was used to determine whether antibodies to a frequently isolated bacterium (Klebsiella pneumoniae) were transferred via milk from mother to pouch young. IgG antibodies were detected in maternal serum, milk and pouch young serum. In young over 70 days, antibody titres were significantly higher than those found in maternal serum, suggesting that the young is capable of producing adult type antibodies to pouch bacteria at this time.

Development of the immune system and immunological protection in marsupial pouch young

At birth the tissues of marsupial immune system are underdeveloped. The young animal is not immunocompetent. Histological and immunohistochemical studies of pouch young epithelial tissues provide a clear picture of tissue development but the timing of onset of immunocompetence awaits definition. The survival of the neonatal marsupial in a microbially rich environment is dependent on maternal strategies, including immunoglobulin transfer via milk and, in some species, prenatally via the yolk sac placenta. It is also likely that pouch secretions play a role. This review summarizes our current knowledge of the pathway of immunological development in marsupials and the protection and threats afforded by the pouch environment.

The effect of oestrus and the presence of pouch young on aerobic bacteria isolated from the pouch of the tammar wallaby, Macropus eugenii

Qualitative changes in the culturable, aerobic bacterial flora isolated from the tammar pouch have been documented over the period leading up to oestrus, at the time of anticipated birth and in absence and presence of pouch young of varying ages. In a group of 12 animals studied thirty species of aerobic bacteria were isolated. Twenty five species were found in pouches with no pouch young, 9 in pouches with young less than 3 weeks of age and 9 in pouches containing older animals. Gram positive organisms including Corynebacterium spp., Micrococcus spp. and Staphylococcus spp. were the most frequent isolates, regardless of reproductive status. Whilst Gram-negative rods Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter aerogenes, and Escherichia coli were found in pouches with and without pouch young, but not in pouches close to oestrus, at the time of birth or in the presence of very young animals (< 6 days). While pouches without pouch young displayed the greatest diversity of bacterial species, there were still significant numbers of bacterial species in those containing pouch young. Results suggest that the microbial population of the tammar pouch does not seriously compromise the well-being of the young animal during crucial stages of immunological development. The data are consistent with observations on the microflora of the quokka pouch but not with data from the koala.

Molecular cloning of the cDNA encoding the constant region of the immunoglobulin A heavy chain (C alpha) from a marsupial: Trichosurus vulpecula (common brushtail possum)

A cDNA encoding the brushtail possum immunoglobulin A heavy chain constant region (C alpha) was isolated by screening a mesenteric lymph node cDNA library with a porcine C alpha exon 3 probe. The larger of the two positive clones isolated (Tv4a) consisted of 1325 bp of possum cDNA that included an open reading frame of 1191 bp. Its deduced amino acid sequence had a high degree of sequence identity with known eutherian C alpha sequences. This clone appears to encode the entire possum IgA heavy chain constant region. The possum C alpha sequence had a nucleotide sequence identity of 57.7% with porcine C alpha, 51% with mouse C alpha, 46.7% with dog C alpha and 45.9% with human C alpha2. The corresponding amino acid identities were 46.7, 45.6, 49.4 and 49%, respectively.