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

Weiss, Sesilje; Taggart, David A.; Smith, Ian; Helgen, Kristofer M.; Eisenhofer, Raphael

doi:10.1186/s42523-021-00074-8

“…Taxonomic assignments were confirmed using blast analysis ( blastn 2.11.0+ [48, 49]) against the NCBI nucleotide collection (nt) database (accessed January 2021). Taxonomic lineage was then retrieved from the NCBI taxonomy database using TaxonKit [50] and adjusted to the lowest common ancestor based on percentage identity and e-value score.…”

Section: Methodsmentioning

confidence: 99%

The bacterial biome of ticks and their wildlife hosts at the urban–wildland interface

Egan

¹

,

Taylor

²

,

Banks

³

et al. 2021

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Advances in sequencing technologies have revealed the complex and diverse microbial communities present in ticks (Ixodida). As obligate blood-feeding arthropods, ticks are responsible for a number of infectious diseases that can affect humans, livestock, domestic animals and wildlife. While cases of human tick-borne diseases continue to increase in the northern hemisphere, there has been relatively little recognition of zoonotic tick-borne pathogens in Australia. Over the past 5 years, studies using high-throughput sequencing technologies have shown that Australian ticks harbour unique and diverse bacterial communities. In the present study, free-ranging wildlife (n=203), representing ten mammal species, were sampled from urban and peri-urban areas in New South Wales (NSW), Queensland (QLD) and Western Australia (WA). Bacterial metabarcoding targeting the 16S rRNA locus was used to characterize the microbiomes of three sample types collected from wildlife: blood, ticks and tissue samples. Further sequence information was obtained for selected taxa of interest. Six tick species were identified from wildlife: Amblyomma triguttatum, Ixodes antechini, Ixodes australiensis, Ixodes holocyclus, Ixodes tasmani and Ixodes trichosuri. Bacterial 16S rRNA metabarcoding was performed on 536 samples and 65 controls, generating over 100 million sequences. Alpha diversity was significantly different between the three sample types, with tissue samples displaying the highest alpha diversity (P<0.001). Proteobacteria was the most abundant taxon identified across all sample types (37.3 %). Beta diversity analysis and ordination revealed little overlap between the three sample types (P<0.001). Taxa of interest included Anaplasmataceae , Bartonella , Borrelia , Coxiellaceae , Francisella , Midichloria , Mycoplasma and Rickettsia . Anaplasmataceae bacteria were detected in 17.7% (95/536) of samples and included Anaplasma , Ehrlichia and Neoehrlichia species. In samples from NSW, ‘Ca. Neoehrlichia australis’, ‘Ca. Neoehrlichia arcana’, Neoehrlichia sp. and Ehrlichia sp. were identified. A putative novel Ehrlichia sp. was identified from WA and Anaplasma platys was identified from QLD. Nine rodent tissue samples were positive for a novel Borrelia sp. that formed a phylogenetically distinct clade separate from the Lyme Borrelia and relapsing fever groups. This novel clade included recently identified rodent-associated Borrelia genotypes, which were described from Spain and North America. Bartonella was identified in 12.9% (69/536) of samples. Over half of these positive samples were obtained from black rats (Rattus rattus), and the dominant bacterial species identified were Bartonella coopersplainsensis and Bartonella queenslandensis . The results from the present study show the value of using unbiased high-throughput sequencing applied to samples collected from wildlife. In addition to understanding the sylvatic cycle of known vector-associated pathogens, surveillance work is important to ensure preparedness for potential zoonotic spillover events.

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“…As adaptive immunity does not completely mature until 100 days after birth in some species, the young rely on passive immunity from the milk, rapid development of the innate immune system, and antimicrobial compounds from the pouch for protection against pathogens [78–82]. Antimicrobial compounds expressed in the pouch skin likely contribute to changes in the pouch microbiome throughout lactation in marsupials [83, 84], and may selectively eliminate pathogens via direct antibacterial activity [79, 85, 86].…”

Section: Resultsmentioning

confidence: 99%

A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

Peel

¹

,

Silver

²

,

Brandies

³

et al. 2021

Preprint

2

0

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Biodiversity is declining globally, and Australia has one of the worst extinction records for mammals. The development of sequencing technologies means that genomic approaches are now available as important tools for wildlife conservation and management. Despite this, genome sequences are available for only 5% of threatened Australian species. Here we report the first reference genome for the woylie (Bettongia penicillata ogilbyi), a critically endangered marsupial from Western Australia, and the first genome within the Potoroidae family. The woylie reference genome was generated using Pacific Biosciences HiFi long-reads, resulting in a 3.39 Gbp assembly with a scaffold N50 of 6.49 Mbp and 86.5% complete mammalian BUSCOs. Assembly of a global transcriptome from pouch skin, tongue, heart and blood RNA-seq reads was used to guide annotation with Fgenesh++, resulting in the annotation of 24,655 genes. The woylie reference genome is a valuable resource for conservation, management and investigations into disease-induced decline of this critically endangered marsupial.

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“…Antimicrobial compounds expressed in the pouch skin likely contribute to changes in the pouch microbiome throughout lactation in marsupials [83,84], and may selectively eliminate pathogens via direct antibacterial activity [79,85,86]. genes, comparable to other marsupial genomes [58-60, 63, 87].…”

Section: Transcriptomementioning

confidence: 99%

A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

Peel

¹

,

Silver

²

,

Brandies

³

et al. 2021

View full text Add to dashboard Cite

Biodiversity is declining globally, and Australia has one of the worst extinction records for mammals. The development of sequencing technologies means that genomic approaches are now available as important tools for wildlife conservation and management. Despite this, genome sequences are available for only 5% of threatened Australian species. Here we report the first reference genome for the woylie (Bettongia penicillata ogilbyi), a critically endangered marsupial from Western Australia, and the first genome within the Potoroidae family. The woylie reference genome was generated using Pacific Biosciences HiFi long-reads, resulting in a 3.39 Gbp assembly with a scaffold N50 of 6.49 Mbp and 86.5% complete mammalian BUSCOs. Assembly of a global transcriptome from pouch skin, tongue, heart and blood RNA-seq reads was used to guide annotation with Fgenesh++, resulting in the annotation of 24,655 genes. The woylie reference genome is a valuable resource for conservation, management and investigations into disease-induced decline of this critically endangered marsupial. Subjects Genetics and Genomics, Animal Genetics, Genetics DATA DESCRIPTION Background and contextGlobally, we are experiencing a biodiversity crisis, as more than 1 million species currently face extinction [1]. Australia is one of 17 megadiverse countries [2], and has a high level of endemism, with 87% of mammals, 94% of frogs and 93% of reptiles being endemic to Australia [3]. Despite this, Australia has one of the worst mammal extinction rates in the world, with over 10% of endemic terrestrial mammals driven to extinction within the past 200 years [4]. The International Union for Conservation of Nature (IUCN) currently lists over 1000 Australian animals as critically endangered, endangered or vulnerable as of August 2021 [5], yet genome sequences are only available for 5% of these species. Reference genomes are a valuable conservation tool that allow researchers and managers to answer vital biological questions and inform management policy [6]. Development of new sequencing technologies and their subsequent decrease in cost allows the genomes of threatened species to be sequenced [7-9]. Individual research groups can now assemble highly contiguous genomes, which can then be used to answer various biological, evolutionary and conservation questions [10-12].The woylie, or brush-tailed bettong (Bettongia penicillata ogilbyi, NCBI:txid881300), is a small marsupial of the Potoroidae family (Figure 1) [13]. Marsupials are one of three

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

Cited by 14 publications

References 56 publications

The bacterial biome of ticks and their wildlife hosts at the urban–wildland interface

The bacterial biome of ticks and their wildlife hosts at the urban–wildland interface

A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi

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