Gut microbiota composition in obese and non-obese adult relatives from the highlands of Papua New Guinea
- Jonduo, Marinjho, Wawae, Lorry, Masiria, Geraldine, Suda, Wataru, Hattori, Masahira, Takayasu, Lena, Abdad, Mohammad, Greenhill, Andrew, Horwood, Paul, Pomat, William, Umezaki, Masahiro
- Authors: Jonduo, Marinjho , Wawae, Lorry , Masiria, Geraldine , Suda, Wataru , Hattori, Masahira , Takayasu, Lena , Abdad, Mohammad , Greenhill, Andrew , Horwood, Paul , Pomat, William , Umezaki, Masahiro
- Date: 2020
- Type: Text , Journal article
- Relation: FEMS microbiology letters Vol. 367, no. 19 (2020), p.
- Full Text:
- Reviewed:
- Description: Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
- Authors: Jonduo, Marinjho , Wawae, Lorry , Masiria, Geraldine , Suda, Wataru , Hattori, Masahira , Takayasu, Lena , Abdad, Mohammad , Greenhill, Andrew , Horwood, Paul , Pomat, William , Umezaki, Masahiro
- Date: 2020
- Type: Text , Journal article
- Relation: FEMS microbiology letters Vol. 367, no. 19 (2020), p.
- Full Text:
- Reviewed:
- Description: Obesity is a condition that results from an imbalance between energy intake and expenditure. Recently, obesity has been linked to differences in the composition of gut microbiota. To examine this association in Papua New Guinea (PNG) highlanders, fecal samples were collected from 18 adults; nine obese participants were paired with their non-obese relative. Amplification of the 16S rRNA gene targeting the V1-V2 region was performed on DNA extracts for each participant, with high-quality sequences selected and used for operational taxonomic unit clustering. The data showed Firmicutes and Bacteroidetes were the two dominant phyla, while at genus level Prevotella was the most dominant genus in all of the samples. Nonetheless, statistical evaluation of potential association between nutritional status and bacterial abundance at both phyla and genus levels showed no significant difference. Further studies, ideally in both rural and urban areas, are needed to evaluate the role of the gut microbiome in the occurrence of obesity in PNG and other resource-limited settings. © The Author(s) 2020. Published by Oxford University Press on behalf of FEMS.
Polymyxin resistant bacteria in Australian poultry
- Bean, David, Wigmore, Sarah, Abdul Momin, Muhd, Wareham, David
- Authors: Bean, David , Wigmore, Sarah , Abdul Momin, Muhd , Wareham, David
- Date: 2020
- Type: Text , Journal article
- Relation: Frontiers in Sustainable Food Systems Vol. 4, no. (2020), p. 1-7
- Full Text:
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- Description: Resistance to last-resort antibiotics is significant public health issue. Antibiotic use in animal husbandry may be a driver of resistance that can subsequently be disseminated via the food chain. This study sought to determine the level of polymyxin resistance in Gram-negative pathogens present in Australian poultry, particularly the presence of mobilizable mechanisms of polymyxin resistance. Cloacal swabs from 213 birds were taken in a point prevalence survey from six different farms at a Victorian chicken processing facility. Colistin resistant organisms were recovered by direct plating on CHROMagar COL-APSE media. Bacterial isolates were identified and analyzed by MALDI-TOF, biochemical and genotypic assays. The 213 specimens yielded 57 (26.8%) colistin-resistant Gram-negative organisms, all of which have been previously described as exhibiting intrinsic resistance to polymyxin antibiotics. The most frequent organism was identified as Hafnia paralvei (40/57; 70%). Other colistin-resistant organisms included Aeromonas hydrophila (16%), Myroides odoratus (7%), Alcaligenes faecalis (5%), and Pseudochrobactrum spp. (2%). No mobile colistin resistance (mcr) genes were detected, although the arnA gene was identified in two A. hydrophila isolates and may mediate colistin resistance in these isolates. Intrinsic polymyxin-resistant organisms are widely distributed in the food chain, with over a quarter of the birds tested yielding a polymyxin-resistant organism. However, strains containing mcr genes remain rare in Australian poultry. © Copyright © 2020 Bean, Wigmore, Abdul Momin and Wareham.
- Authors: Bean, David , Wigmore, Sarah , Abdul Momin, Muhd , Wareham, David
- Date: 2020
- Type: Text , Journal article
- Relation: Frontiers in Sustainable Food Systems Vol. 4, no. (2020), p. 1-7
- Full Text:
- Reviewed:
- Description: Resistance to last-resort antibiotics is significant public health issue. Antibiotic use in animal husbandry may be a driver of resistance that can subsequently be disseminated via the food chain. This study sought to determine the level of polymyxin resistance in Gram-negative pathogens present in Australian poultry, particularly the presence of mobilizable mechanisms of polymyxin resistance. Cloacal swabs from 213 birds were taken in a point prevalence survey from six different farms at a Victorian chicken processing facility. Colistin resistant organisms were recovered by direct plating on CHROMagar COL-APSE media. Bacterial isolates were identified and analyzed by MALDI-TOF, biochemical and genotypic assays. The 213 specimens yielded 57 (26.8%) colistin-resistant Gram-negative organisms, all of which have been previously described as exhibiting intrinsic resistance to polymyxin antibiotics. The most frequent organism was identified as Hafnia paralvei (40/57; 70%). Other colistin-resistant organisms included Aeromonas hydrophila (16%), Myroides odoratus (7%), Alcaligenes faecalis (5%), and Pseudochrobactrum spp. (2%). No mobile colistin resistance (mcr) genes were detected, although the arnA gene was identified in two A. hydrophila isolates and may mediate colistin resistance in these isolates. Intrinsic polymyxin-resistant organisms are widely distributed in the food chain, with over a quarter of the birds tested yielding a polymyxin-resistant organism. However, strains containing mcr genes remain rare in Australian poultry. © Copyright © 2020 Bean, Wigmore, Abdul Momin and Wareham.
Ant community responses to farmland use and revegetation in a fragmented agricultural landscape
- Ng, Katherine, Nowrouzi, Somayeh, Staunton, Kyran, Barton, Philip, Driscoll, Don
- Authors: Ng, Katherine , Nowrouzi, Somayeh , Staunton, Kyran , Barton, Philip , Driscoll, Don
- Date: 2021
- Type: Text , Journal article
- Relation: Agriculture Ecosystems & Environment Vol. 311, no. (May 2021), p. 8
- Full Text:
- Reviewed:
- Description: Recent alarming losses of insects from agricultural landscapes in multiple countries around the world have brought into sharp focus the urgent need to identify ways to manage these landscapes to avoid further biodiversity decline. Identifying the drivers of insect declines, such as land use change, is critical to this effort. We examined ant communities at the interface between remnant vegetation patches and three adjoining farmland types (wheat crop, rested from cropping and restoration plantings) in a fragmented landscape in temperate Australia. We asked: do ant communities and occurrence of individual species differ between remnant patches and farmlands with more intensive farmland use (restoration plantings < rested farmlands < wheat crop)? We recorded 13,283 ants belonging to 102 species from 30 genera. Excluding 21 singletons, 27 species only occurred in remnant patches compared to ten species found only in farmlands. Ant community composition in wheat crop and rested farmlands significantly differed from their adjacent remnant patches and were more homogeneous. In contrast, ant communities from restoration plantings in farmland were not significantly different in composition from those in the adjacent remnant patch. The large, aggressive Australian meat ant (Iridomyrmex purpureus) showed significantly higher occurrence in the remnant patch than all farmland types, and we suggest that the absence of this strongly interacting species from farmlands may have contributed to biotic homogenisation. Our findings show that native vegetation provides crucial habitat resources for many ant species that are not provided by farmlands, and native plantings can, in some cases, ameliorate negative effects of farmland clearing over relatively short time scales (<7 years). Agricultural intensification that involves loss of remnant native vegetation or reduced revegetation will contribute to ongoing losses and changes to ant biodiversity in farming landscapes. However, replanting native vegetation can lead to rapid restoration, signifying a possible simple remedy to insect declines.
- Authors: Ng, Katherine , Nowrouzi, Somayeh , Staunton, Kyran , Barton, Philip , Driscoll, Don
- Date: 2021
- Type: Text , Journal article
- Relation: Agriculture Ecosystems & Environment Vol. 311, no. (May 2021), p. 8
- Full Text:
- Reviewed:
- Description: Recent alarming losses of insects from agricultural landscapes in multiple countries around the world have brought into sharp focus the urgent need to identify ways to manage these landscapes to avoid further biodiversity decline. Identifying the drivers of insect declines, such as land use change, is critical to this effort. We examined ant communities at the interface between remnant vegetation patches and three adjoining farmland types (wheat crop, rested from cropping and restoration plantings) in a fragmented landscape in temperate Australia. We asked: do ant communities and occurrence of individual species differ between remnant patches and farmlands with more intensive farmland use (restoration plantings < rested farmlands < wheat crop)? We recorded 13,283 ants belonging to 102 species from 30 genera. Excluding 21 singletons, 27 species only occurred in remnant patches compared to ten species found only in farmlands. Ant community composition in wheat crop and rested farmlands significantly differed from their adjacent remnant patches and were more homogeneous. In contrast, ant communities from restoration plantings in farmland were not significantly different in composition from those in the adjacent remnant patch. The large, aggressive Australian meat ant (Iridomyrmex purpureus) showed significantly higher occurrence in the remnant patch than all farmland types, and we suggest that the absence of this strongly interacting species from farmlands may have contributed to biotic homogenisation. Our findings show that native vegetation provides crucial habitat resources for many ant species that are not provided by farmlands, and native plantings can, in some cases, ameliorate negative effects of farmland clearing over relatively short time scales (<7 years). Agricultural intensification that involves loss of remnant native vegetation or reduced revegetation will contribute to ongoing losses and changes to ant biodiversity in farming landscapes. However, replanting native vegetation can lead to rapid restoration, signifying a possible simple remedy to insect declines.
Insights from long-term shorebird monitoring for tracking change in ecological character of Australasian Ramsar sites
- Hansen, Birgita, Szabo, Judit, Fuller, Richard, Clemens, Robert, Rogers, Danny, Milton, David
- Authors: Hansen, Birgita , Szabo, Judit , Fuller, Richard , Clemens, Robert , Rogers, Danny , Milton, David
- Date: 2021
- Type: Text , Journal article
- Relation: Biological Conservation Vol. 260, no. (2021), p.
- Full Text:
- Reviewed:
- Description: The Ramsar Convention is the centrepiece of international efforts for wetland conservation, aiming to maintain the ecological character of wetlands through holistic ecosystem management. Here, we review studies on shorebird populations at individual Australasian Ramsar sites and compare these against original listings under Criterion 6 to determine if there have been potential changes in ecological character. One to 12 migratory shorebird species have declined at four New Zealand and 18 Australian Ramsar sites over a 12 to 36-year period, resulting in 22 species (at 13 sites) no longer reaching Criterion 6 thresholds for Ramsar designation. In addition, 10 species at six Australian sites had exceeded the Limits of Acceptable Change. Despite these concerning results, there were remarkably few published site-based determinations of listed shorebird species' trends (and even fewer that were ≤5 years old). This is especially surprising since shorebird populations are regularly monitored at 27 out of 35 Australasian Ramsar sites (listed on the basis of one or more shorebird species). Thus, despite the volume of data available for analysis, long-term shorebird monitoring provides only limited insights about Ramsar ecological character. The value of these data would be greatly enhanced through complementary monitoring of other ecological characters at sites, particularly where shorebird populations provide early warning signs of potential deterioration. The main impediment to achieving a good understanding of how Ramsar sites are changing in Australasia appears to be a lack of analysis and centralised system for data and analytics, rather than a lack of monitoring data. © 2021 Elsevier Ltd
- Authors: Hansen, Birgita , Szabo, Judit , Fuller, Richard , Clemens, Robert , Rogers, Danny , Milton, David
- Date: 2021
- Type: Text , Journal article
- Relation: Biological Conservation Vol. 260, no. (2021), p.
- Full Text:
- Reviewed:
- Description: The Ramsar Convention is the centrepiece of international efforts for wetland conservation, aiming to maintain the ecological character of wetlands through holistic ecosystem management. Here, we review studies on shorebird populations at individual Australasian Ramsar sites and compare these against original listings under Criterion 6 to determine if there have been potential changes in ecological character. One to 12 migratory shorebird species have declined at four New Zealand and 18 Australian Ramsar sites over a 12 to 36-year period, resulting in 22 species (at 13 sites) no longer reaching Criterion 6 thresholds for Ramsar designation. In addition, 10 species at six Australian sites had exceeded the Limits of Acceptable Change. Despite these concerning results, there were remarkably few published site-based determinations of listed shorebird species' trends (and even fewer that were ≤5 years old). This is especially surprising since shorebird populations are regularly monitored at 27 out of 35 Australasian Ramsar sites (listed on the basis of one or more shorebird species). Thus, despite the volume of data available for analysis, long-term shorebird monitoring provides only limited insights about Ramsar ecological character. The value of these data would be greatly enhanced through complementary monitoring of other ecological characters at sites, particularly where shorebird populations provide early warning signs of potential deterioration. The main impediment to achieving a good understanding of how Ramsar sites are changing in Australasia appears to be a lack of analysis and centralised system for data and analytics, rather than a lack of monitoring data. © 2021 Elsevier Ltd
Livestock data – is it there and is it FAIR? A systematic review of livestock farming datasets in Australia
- Bahlo, Christiane, Dahlhaus, Peter
- Authors: Bahlo, Christiane , Dahlhaus, Peter
- Date: 2021
- Type: Text , Journal article
- Relation: Computers and Electronics in Agriculture Vol. 188, no. (2021), p.
- Full Text:
- Reviewed:
- Description: The global adoption of the FAIR principles for scientific data: findable, accessible, interoperable and reusable, has been relatively slow in agriculture, compared to other disciplines. A recent review of the literature showed that the use of precision farming technologies and the development and adoption of open data standards was particularly low in extensive livestock farming. However, a plethora of public datasets exist that have the potential to be used to inform precision farming decision tools. Using extensive livestock farming in Australia as example, we investigate the quantity and quality of datasets available via a systematic dataset review. This systematic review of datasets begins with a search of open data catalogues and querying these to find datasets. Software scripts are developed and used to query the Application Programming Interfaces (APIs) of many of the large data catalogues in Australia, while catalogues without public APIs are queried manually via available web portals. Following the systematic search, a combined list of all datasets is collated and tested for FAIRness and other quality metrics. The contribution of this work is the resulting overview of the state of open datasets within the livestock farming domain on the one hand, but also the development of a systematic dataset search strategy, reusable methods and software scripts. © 2021 Elsevier B.V.
- Authors: Bahlo, Christiane , Dahlhaus, Peter
- Date: 2021
- Type: Text , Journal article
- Relation: Computers and Electronics in Agriculture Vol. 188, no. (2021), p.
- Full Text:
- Reviewed:
- Description: The global adoption of the FAIR principles for scientific data: findable, accessible, interoperable and reusable, has been relatively slow in agriculture, compared to other disciplines. A recent review of the literature showed that the use of precision farming technologies and the development and adoption of open data standards was particularly low in extensive livestock farming. However, a plethora of public datasets exist that have the potential to be used to inform precision farming decision tools. Using extensive livestock farming in Australia as example, we investigate the quantity and quality of datasets available via a systematic dataset review. This systematic review of datasets begins with a search of open data catalogues and querying these to find datasets. Software scripts are developed and used to query the Application Programming Interfaces (APIs) of many of the large data catalogues in Australia, while catalogues without public APIs are queried manually via available web portals. Following the systematic search, a combined list of all datasets is collated and tested for FAIRness and other quality metrics. The contribution of this work is the resulting overview of the state of open datasets within the livestock farming domain on the one hand, but also the development of a systematic dataset search strategy, reusable methods and software scripts. © 2021 Elsevier B.V.