ORCID Profile
0000-0002-3843-0749
Current Organisations
IT University of Copenhagen
,
University of Adelaide
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Research Square Platform LLC
Date: 08-09-2022
DOI: 10.21203/RS.3.RS-1955526/V2
Abstract: Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genome completeness and function fullness, and provide baseline knowledge to guide efforts to correct for this new-found bias in functional metagenomic analyses.
Publisher: Springer Science and Business Media LLC
Date: 06-01-2021
DOI: 10.1186/S42523-020-00068-Y
Abstract: Herbivorous mammals co-opt microbes to derive energy and nutrients from diets that are recalcitrant to host enzymes. Recent research has found that captive management—an important conservation tool for many species—can alter the gut microbiota of mammals. Such changes could negatively impact the ability of herbivorous mammals to derive energy from their native diets, and ultimately reduce host fitness. To date, nothing is known of how captivity influences the gut microbiota of the Southern Hairy-nosed Wombat (SHNW), a large herbivorous marsupial that inhabits South Australia. Here, using 16S rRNA gene sequencing, we characterized the faecal microbiota of SHNWs in captivity and from three wild populations, two from degraded habitats and one from an intact native grass habitat. We found that captive SHNWs had gut microbiota that were compositionally different and less erse compared to wild SHNWs. There were major differences in gut microbiota community membership between captive and wild animals, both in statistically significant changes in relative abundance of microbes, and in the presence/absence of microbes. We also observed differences in microbial composition between wild populations, with the largest difference associated with native vs. degraded habitat. These results suggest that captivity has a major impact on the gut microbiota of SHNWs, and that different wild populations harbour distinct microbial compositions. Such findings warrant further work to determine what impacts these changes have on the fitness of SHNWs, and whether they could be manipulated to improve future management of the species.
Publisher: Research Square Platform LLC
Date: 12-08-2022
DOI: 10.21203/RS.3.RS-1955526/V1
Abstract: Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of MAGs has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genome completeness and function fullness, and provide baseline knowledge to guide efforts to correct for this new-found bias in functional metagenomic analyses.
Publisher: PeerJ
Date: 13-03-2019
DOI: 10.7717/PEERJ.6594
Abstract: The field of palaeomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic s les. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to short DNA fragment lengths routinely identified within ancient specimens ( bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ∼100,000 years of genomic ergence minimally impact alignment-based classification. We also test four different reference databases and find that database choice can significantly bias the results of alignment-based taxonomic classification in ancient metagenomic studies. Finally, we perform a reanalysis of previously published ancient dental calculus data, increasing the number of microbial DNA sequences assigned taxonomically by an average of 64.2-fold and identifying microbial species previously unidentified in the original study. Overall, this study enhances our understanding of how ancient DNA characteristics influence alignment-based taxonomic classification of ancient microorganisms and provides recommendations for future palaeomicrobiological studies.
Publisher: Research Square Platform LLC
Date: 20-04-2022
DOI: 10.21203/RS.3.RS-1567786/V1
Abstract: Background Gut microbiota studies often rely on a single s le taken per in idual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-in idual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala ( Phascolarctos cinereus ) gut microbiota through time. Here, we characterise the gut microbiota from faecal s les collected at 8 timepoints over a month for a captive population of South Australian koalas (n in iduals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n in iduals = 5). Results Using 16S rRNA gene sequencing, we found that microbial ersity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each in idual still maintained a distinct microbial composition. Per koala, an average of 57 (± 16) licon sequence variants (ASVs) were detected across all time points these ASVs accounted for an average of 97% (± 1.9%) of the faecal microbial community per koala. Conclusion The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
Publisher: Elsevier BV
Date: 02-2019
DOI: 10.1016/J.TIM.2018.11.003
Abstract: Next-generation sequencing approaches in microbiome research have allowed surveys of microbial communities, their genomes, and their functions with higher sensitivity than ever before. However, this sensitivity is a double-edged sword because these tools also efficiently detect contaminant DNA and cross-contamination, which can confound the interpretation of microbiome data. Therefore, there is an urgent need to integrate key controls into microbiome research to improve the integrity of microbiome studies. Here, we review how contaminant DNA and cross-contamination arise within microbiome studies and discuss their negative impacts, especially during the analysis of low microbial biomass s les. We then identify several key measures that researchers can implement to reduce the impact of contaminant DNA and cross-contamination during microbiome research. We put forward a set of minimal experimental criteria, the 'RIDE' checklist, to improve the validity of future low microbial biomass research.
Publisher: Informa UK Limited
Date: 13-11-2201
Publisher: PeerJ
Date: 23-02-2022
DOI: 10.7717/PEERJ.12982
Abstract: Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on s les collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat ( Vombatus ursinus ) and a single southern hairy-nosed wombat ( Lasiorhinus latifrons ). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat in iduals, we observed a trend of increasing microbial ersity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal s les). Surprisingly, only 10.6% (98) and 18.8% (206) of licon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal s les may have limitations in capturing the ersity of these communities. While faeces are still a valuable and effective means of characterising the distal colon microbiota, future work seeking to better understand how GI microbiota impact the energy economy of wombats (and potentially other hindgut-fermenting mammals) may need to take gut biogeography into account.
Publisher: Frontiers Media SA
Date: 30-06-2022
DOI: 10.3389/FMICB.2022.687115
Abstract: The gut microbiome plays a vital role in health and wellbeing of animals, and an increasing number of studies are investigating microbiome changes in wild and managed populations to improve conservation and welfare. The short-beaked echidna ( Tachyglossus aculeatus ) is an iconic Australian species, the most widespread native mammal, and commonly held in zoos. Echidnas are cryptic animals, and much is still unknown about many aspects of their biology. Furthermore, some wild echidna populations are under threat, while echidnas held in captivity can have severe gastric health problems. Here, we used citizen science and zoos to collect echidna scats from across Australia to perform the largest gut microbiome study on any native Australian animal. Using 16S rRNA gene metabarcoding of scat s les, we characterised and compared the gut microbiomes of echidnas in wild ( n = 159) and managed ( n = 44) populations, which were fed four different diets. Wild echidna s les were highly variable, yet commonly dominated by soil and plant-fermenting bacteria, while echidnas in captivity were dominated by gut commensals and plant-fermenting bacteria, suggesting plant matter may play a significant role in echidna diet. This work demonstrates significant differences between zoo held and wild echidnas, as well as managed animals on different diets, revealing that diet is important in shaping the gut microbiomes in echidnas. This first analysis of echidna gut microbiome highlights extensive microbial ersity in wild echidnas and changes in microbiome composition in managed populations. This is a first step towards using microbiome analysis to better understand diet, gastrointestinal biology, and improve management in these iconic animals.
Publisher: PeerJ
Date: 23-01-2023
DOI: 10.7717/PEERJ.14598
Abstract: Gut microbiota studies often rely on a single s le taken per in idual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-in idual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala ( Phascolarctos cinereus ) gut microbiota through time. Here, we characterise the gut microbiota from faecal s les collected at eight timepoints over a month for a captive population of South Australian koalas ( n in iduals = 7), and monthly over 7 months for a wild population of New South Wales koalas ( n in iduals = 5). Using 16S rRNA gene sequencing, we found that microbial ersity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each in idual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) licon sequence variants (ASVs) were detected across all time points these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
Publisher: Springer Science and Business Media LLC
Date: 25-01-2021
DOI: 10.1186/S42523-021-00074-8
Abstract: 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 s les from animals at different reproductive stages. Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and ersity between the body sites tested, as well as between pouch s les from different reproductive stages. The pouches of reproductively active females had drastically lower microbial ersity (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. 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.
Publisher: Wiley
Date: 13-05-2020
Publisher: eLife Sciences Publications, Ltd
Date: 21-06-2019
DOI: 10.7554/ELIFE.48493
Abstract: Modern microorganisms growing in fossils provide major challenges for researchers trying to detect ancient molecules in the same fossils.
Publisher: Cold Spring Harbor Laboratory
Date: 06-10-2023
Publisher: American Society for Microbiology
Date: 25-08-2016
Publisher: Springer Science and Business Media LLC
Date: 13-09-2022
DOI: 10.1186/S13071-022-05452-Y
Abstract: Sarcoptes scabiei is globally distributed and one of the most impactful mammalian ectoparasites. Sarcoptic mange, caused by infection with S. scabiei , causes disruption of the epidermis and its bacterial microbiota, but its effects on host fungal microbiota and on the microbiota of marsupials in general have not been studied. Here, we (i) examine bacterial and fungal microbiota changes associated with mange in wild bare-nosed wombats (BNWs) and (ii) evaluate whether opportunistic pathogens are potentiated by S. scabiei infection in this species. Using Amplicon Sequencing of the 16S rRNA and ITS2 rDNA genes, we detected skin microbiota changes of the bare-nosed wombat ( Vombatus ursinus ). We compared the alpha and beta ersity among healthy, moderate, and severe disease states using ANOVA and PERMANOVA with nesting. Lastly, we identified taxa that differed between disease states using analysis of composition of microbes (ANCOM) testing. We detected significant changes in the microbial communities and ersity with mange in BNWs. Severely affected BNWs had lower licon sequence variant (ASV) richness compared to that of healthy in iduals, and the microbial communities were significantly different between disease states with higher relative abundance of potentially pathogenic microbial taxa in mange-affected BNWs including Staphylococcus sciuri , Corynebacterium spp., Brevibacterium spp., Brachybacterium spp., and Pseudogymnascus spp. and Debaryomyces spp. This study represents the first investigation of microbial changes in association with sarcoptic mange in a marsupial host, as well as the first investigation of fungal microbial changes on the skin of any host suffering from sarcoptic mange. Our results are broadly consistent with bacterial microbiota changes observed in humans, pigs, canids, and Iberian ibex, suggesting the epidermal microbial impacts of mange may be generalisable across host species. We recommend that future studies investigating skin microbiota changes include both bacterial and fungal data to gain a more complete picture of the effects of sarcoptic mange.
Publisher: Cold Spring Harbor Laboratory
Date: 28-01-2022
DOI: 10.1101/2022.01.26.472964
Abstract: This manuscript is discussing the method of Weyrich et al ., 2017, “Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus”. When studying the dietary profile of a Neanderthal specimen from El Sidrón cave (Spain) by sequencing ancient DNA present in calcified dental plaque (calculus) the authors identified a wide-range of potential food sources, including woolly rhinoceros, mushrooms, pine nuts, and moss – namely the less-than-abundant model species Physcomitrium patens . We doubted that Neanderthals were actually eating P. patens . By analyzing the ancient DNA reads using different mapping methods, we show likely a misinterpretation based on the previously used methods. The probability of Neanderthals eating P. patens is the same as eating rice or tomato. However, neither crop was grown in Europe at the time Neanderthals thrived.
Publisher: Springer Science and Business Media LLC
Date: 09-11-2021
DOI: 10.1038/S43705-021-00070-8
Abstract: Sedimentary ancient DNA ( sed aDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sed aDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising ex les are 18S-V9 rRNA (~121–130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as lification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment s les (up to ~11 000 years old) and applied both a metabarcoding ( 18S-V9 rRNA , diat-rbcL ) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and over lification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros , Thalassiosira and Pseudo-nitzschia . Our results are relevant to sed aDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.
Publisher: MDPI AG
Date: 26-02-2018
DOI: 10.3390/GENES9030122
No related grants have been discovered for Raphael Eisenhofer.