ORCID Profile
0000-0001-5243-4634
Current Organisations
The Pennsyvlania State University
,
University of Adelaide
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Publisher: Wiley
Date: 10-2019
DOI: 10.1111/MEC.15240
Abstract: Urbanisation is one of the most significant threats to bio ersity, due to the rapid and large‐scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non‐model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non‐model species – the eastern water dragon ( Intellagama lesueurii ) in Queensland, Australia. City dragons exhibit a more erse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen‐15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human‐altered landscapes.
Publisher: Wiley
Date: 29-04-2019
Publisher: The Royal Society
Date: 05-10-2020
Abstract: While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus s les and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain ersity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species— Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
Publisher: Wiley
Date: 17-02-2023
DOI: 10.1002/AJPA.24714
Abstract: Retraction: Cortez, A. D., Lippert, D., Davis, J. L., Nicholas, G., Malhi, R. S., Weyrich, L. S., Claw, K. G., Bader, A. C., & Colwell, C. (2023). Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples. American Journal of Biological Anthropology. 0.1002/ajpa.24714 . The above article, published online on 17 February 2023 in Wiley Online Library ( wileyonlinelibrary.com ), has been retracted by agreement between the authors, the journal Editor in Chief, Trudy Turner, and Wiley Periodicals LLC. The retraction has been agreed due to a former collaborator voiding permission for use of their early contribution to the team project.
Publisher: Cold Spring Harbor Laboratory
Date: 18-06-2021
DOI: 10.1101/2021.06.18.448749
Abstract: The planting and conservation of bio erse habitat in urban contexts has been proposed as a public health intervention aimed at reducing the prevalence of non-communicable diseases via microbiome rewilding (Mills et al. 2017 Mills et al. 2019). However, our understanding of the effect of urban bio ersity interventions on the human microbiota remains limited, especially on the skin (Hui et al. 2019 Roslund et al. 2020) and in the context of permanent green spaces (Lehtimäki et al. 2018 Selway et al. 2020). Here, we test the short-term response of experimentally disturbed bacterial communities on the skin of healthy children exposed to different school environments – either a ‘classroom’, a ‘sports field’, or a bio erse ‘forest’ – to understand how exposures to different types of bio ersity may influence skin microbiota. Children exposed to the ‘forest’ had significantly increased skin microbiota ersity when compared to pre-exposure, an effect that increased over three days suggesting long-term effects. The microbiota on children exposed to the ‘forest’ had the largest structural and compositional community change compared to children exposed to ‘sports fields’, which in turn was larger than those who remained in ‘classrooms’. Children exposed to ‘sports fields’ and ‘forests’ also acquired new core bacteria after exposure to green spaces, potentially buffering against disturbances to the skin microbiota’s ersity, while in iduals who remained in the ‘classroom’ lost microbes throughout the experiment. Overall, we conclude that urban green spaces can have an enriching influence on the ersity of skin microbiota, including core members shared between all children. These findings have important implications for the design and construction of new school yards and public spaces with respect to bio ersity, health, and human microbiota.
Publisher: Oxford University Press (OUP)
Date: 04-2014
Publisher: Elsevier BV
Date: 11-2014
DOI: 10.1016/J.FSIGEN.2014.07.014
Abstract: Soil analysis, such as mineralogy, geophysics, texture and colour, are commonly used in forensic casework to link a suspect to a crime scene. However, DNA analysis can also be applied to characterise the vast ersity of organisms present in soils. DNA metabarcoding and high-throughput sequencing (HTS) now offer a means to improve discrimination between forensic soil s les by identifying in idual taxa and exploring non-culturable microbial species. Here, we compare the small-scale reproducibility and resolution of four molecular markers targeting different taxa (bacterial 16S rRNA, eukaryotic18S rRNA, plant trnL intron and fungal internal transcribed spacer I (ITS1) rDNA) to distinguish two s le sites. We also assess the background DNA level associated with each marker and examine the effects of filtering Operational Taxonomic Units (OTUs) detected in extraction blank controls. From this study, we show that non-bacterial taxa in soil, particularly fungi, can provide the greatest resolution between the sites, whereas plant markers may be problematic for forensic discrimination. ITS and 18S markers exhibit reliable lification, and both show high discriminatory power with low background DNA levels. The 16S rRNA marker showed comparable discriminatory power post filtering however, presented the highest level of background DNA. The discriminatory power of all markers was increased by applying OTU filtering steps, with the greatest improvement observed by the removal of any sequences detected in extraction blanks. This study demonstrates the potential use of multiple DNA markers for forensic soil analysis using HTS, and identifies some of the standardisation and evaluation steps necessary before this technique can be applied in casework.
Publisher: Wiley
Date: 14-05-2014
Abstract: Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of ersity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR- lification bias, as well as sufficient sequence ergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers lified in silico 90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR- lification bias, typically lifying a greater percentage of Lepidoptera and Diptera species, while failing to lify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR- lified the blend using five primer sets, targeting either COI or 16S, with high-throughput licon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers.
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 11-2012
Publisher: Microbiology Society
Date: 27-01-2022
Abstract: Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial bio ersity to benefit human health. Exposure to urban microbial bio ersity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via bio ersity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e. ersity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK Haikou, China and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil s les and assessing bacterial ersity. We characterized these green spaces as having ‘low’ or ‘high’ vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and ersity around the world. Within cities, we observed significantly different alpha and beta ersities between vegetation complexities however, these results varied between cities. Rare genera ( % relative abundance in idually, on average 35% relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.
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: 07-09-2021
DOI: 10.1038/S41598-021-97057-1
Abstract: Macropod progressive periodontal disease (MPPD) is a necrotizing, polymicrobial, inflammatory disease commonly diagnosed in captive macropods. MPPD is characterized by gingivitis associated with dental plaque formation, which progresses to periodontitis and then to osteomyelitis of the mandible or maxilla. However, the underlying microbial causes of this disease remain poorly understood. In this study, we collected 27 oral plaque s les and associated clinical records from 22 captive Macropodidae and Potoroidae in iduals that were undergoing clinical examination at Adelaide and Monarto Zoos in South Australia (15 healthy, 7 gingivitis and 5 periodontitis-osteomyelitis s les). The V3-V4 region of the 16S ribosomal RNA gene was sequenced using an Illumina Miseq to explore links between MPPD and oral bacteria in these animals. Compositional differences were detected between the microbiota of periodontitis-osteomyelitis cases compared to healthy s les (p-value with Bonferroni correction 0.01), as well as gingivitis cases compared to healthy s les (p-value with Bonferroni correction 0.05) using Permutational Multivariate Analysis of Variance (PERMANOVA). An overabundance of Porphyromonas , Fusobacterium , and Bacteroides taxa was also identified in animals with MPPD compared to healthy in iduals using linear discriminant analysis effect size (LEfSe p = 0.05). An increased abundance of Desulfomicrobium also was detected in MPPD s les (LEfSe p 0.05) , which could potentially reflect differences in disease progression. This is the first microbiota analysis of MPPD in captive macropods, and these results support a polymicrobial pathogenesis of MPPD, suggesting that the microbial interactions underpinning MPPD may be more complex than previously documented.
Publisher: Public Library of Science (PLoS)
Date: 12-10-2012
Publisher: Wiley
Date: 10-10-2023
DOI: 10.1111/FWB.14182
Publisher: Cold Spring Harbor Laboratory
Date: 22-02-2021
DOI: 10.1101/2021.02.21.432167
Abstract: Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial bio ersity to benefit human health. Exposure to urban microbial bio ersity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via bio ersity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e., ersity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK Haikou, China and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil s les and assessing bacterial ersity. We characterized these green spaces as having ‘low’ or ‘high’ vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and ersity around the world. Within cities, we observed significantly different alpha and beta ersities between vegetation complexities however, these results varied between cities. Rare genera ( 1 % relative abundance in idually, on average 35 % relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.
Publisher: Springer Science and Business Media LLC
Date: 12-11-2020
Publisher: Informa UK Limited
Date: 2021
Publisher: Informa UK Limited
Date: 13-11-2201
Publisher: American Society for Microbiology
Date: 09-2009
DOI: 10.1128/IAI.01362-08
Abstract: Despite the fact that closely related bacteria can cause different levels of disease, the genetic changes that cause some isolates to be more pathogenic than others are generally not well understood. We use a combination of approaches to determine which factors contribute to the increased virulence of a Bordetella bronchiseptica lineage. A strain isolated from a host with B. bronchiseptica -induced disease, strain 1289, was 60-fold more virulent in mice than one isolated from an asymptomatically infected host, strain RB50. Transcriptome analysis and quantitative reverse transcription-PCR showed that the type III secretion system (TTSS) genes were more highly expressed by strain 1289 than strain RB50. Compared to strain RB50, strain 1289 exhibited greater TTSS-mediated cytotoxicity of a mammalian cell line. Additionally, we show that the increase in virulence of strain 1289 compared to that of RB50 was partially attributable to the TTSS. Using multilocus sequence typing, we identified another strain from the same lineage as strain 1289. Similar to strain 1289, we implicate the TTSS in the increased virulence of this strain. Together, our data suggest that the TTSS is involved in the increased virulence of a B. bronchiseptica lineage which appears to be disproportionately associated with disease. These data are consistent with the view that B. bronchiseptica lineages can have different levels of virulence, which may contribute to this species' ability to cause different severities of respiratory disease.
Publisher: Elsevier BV
Date: 02-2015
DOI: 10.1016/J.JHEVOL.2014.06.018
Abstract: Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA s ling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine.
Publisher: Wiley
Date: 1994
DOI: 10.1002/AJPA.23637
Abstract: Nearly all Indigenous populations today suffer from worse health than their non-Indigenous counterparts, and despite interventions against known factors, this health "gap" has not improved. The human microbiome-the beneficial, erse microbial communities that live on and within the human body-is a crucial component in developing and maintaining normal physiological health. Disrupting this ecosystem has repercussions for microbial functionality, and thus, human health. In this article, we propose that modern-day Indigenous population health may suffer from disrupted microbial ecosystems as a consequence of historical colonialism. Colonialism may have interrupted the established relationships between the environment, traditional lifeways, and microbiomes, altering the Indigenous microbiome with detrimental health consequences.
Publisher: Wiley
Date: 05-1969
DOI: 10.1111/MEC.15055
Abstract: Microalgal bloom events can cause major ecosystem disturbances, devastate local marine economies, and endanger public health. Therefore, detecting and monitoring harmful microalgal taxa is essential to ensure effective risk management in waterways used for fisheries, aquaculture, recreational activity, and shipping. To fully understand the current status and future direction of algal bloom distributions, we need to know how populations and ecosystems have changed over time. This baseline knowledge is critical for predicting ecosystem responses to future anthropogenic change and will assist in the future management of coastal ecosystems. We explore a NGS metabarcoding approach to rapidly identify potentially harmful microalgal taxa in 63 historic and modern Australian marine port and ballast tank sediment s les. The results provide a record of past microalgal distribution and important baseline data that can be used to assess the efficacy of shipping guidelines, nutrient pollution mitigation, and predict the impact of climate change. Critically, eDNA surveys of archived sediments were able to detect harmful algal taxa that do not produce microscopic fossils, such as Chattonella, Heterosigma, Karlodinium, and Noctiluca. Our data suggest a potential increase in Australian harmful microalgal taxa over the past 30 years, and confirm ship ballast tanks as key dispersal vectors. These molecular mapping tools will assist in the creation of policies aimed at reducing the global increase and spread of harmful algal taxa and help prevent economic and public-health problems caused by harmful algal blooms.
Publisher: Elsevier BV
Date: 04-2023
Publisher: Oxford University Press (OUP)
Date: 13-11-2014
Publisher: Elsevier BV
Date: 05-2014
DOI: 10.1016/J.SCIJUS.2014.02.006
Abstract: Soil is commonly used in forensic casework to provide discriminatory power to link a suspect to a crime scene. Standard analyses examine the intrinsic properties of soils, including mineralogy, geophysics, texture and colour however, soils can also support a vast amount of organisms, which can be examined using DNA fingerprinting techniques. Many previous genetic analyses have relied on patterns of fragment length variation produced by lification of unidentified taxa in the soil extract. In contrast, the development of advanced DNA sequencing technologies now provides the ability to generate a detailed picture of soil microbial communities and the taxa present, allowing for improved discrimination between s les. However, DNA must be efficiently extracted from the complex soil matrix to achieve accurate and reproducible DNA sequencing results, and extraction efficacy is highly dependent on the soil type and method used. As a result, a consideration of soil properties is important when estimating the likelihood of successful DNA extraction. This would include a basic understanding of soil components, their interactions with DNA molecules and the factors that affect such interactions. This review highlights some important considerations required prior to DNA extraction and discusses the use of common chemical reagents in soil DNA extraction protocols to achieve maximum efficacy. Together, the information presented here is designed to facilitate informed decisions about the most appropriate s ling and extraction methodology, relevant both to the soil type and the details of a specific forensic case, to ensure sufficient DNA yield and enable successful analysis.
Publisher: Informa UK Limited
Date: 2013
DOI: 10.1080/08989621.2013.749742
Abstract: Limited time dedicated to each training areas, irrelevant case-studies, and ethics "checklists" have resulted in bare-bones Responsible Conduct of Research (RCR) training for present biomedical graduate student researchers. Here, we argue that science graduate students be taught classical ethical theory, such as virtue ethics, consequentialist theory, and deontological theory, to provide a basic framework to guide researchers through ethically complex situations and examine the applicability, implications, and societal ramifications of their research. Using a relevant biomedical research ex le to illustrate this point, we argue that proper ethics training for graduate student researchers not only will enhance current RCR training, but train more creative, responsible scientists.
Publisher: Springer Science and Business Media LLC
Date: 17-02-2013
DOI: 10.1038/NG.2536
Publisher: Informa UK Limited
Date: 30-11-2017
No related grants have been discovered for Laura Weyrich.