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Moore KH, Ognenovska S, Chua XY, Chen Z, Hicks C, El-Assaad F, te West N, El-Omar E. Change in microbiota profile after vaginal estriol cream in postmenopausal women with stress incontinence. Front Microbiol 2024; 15:1302819. [PMID: 38505551 PMCID: PMC10948564 DOI: 10.3389/fmicb.2024.1302819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Introduction Vaginal estrogen is a treatment for genitourinary symptoms of menopause (GSM), which comprises vaginal atrophy and urinary dysfunction, including incontinence. Previous studies show that estrogen therapy promotes lactobacilli abundance and is associated with reduced GSM symptoms, including reduction of stress incontinence. However, detailed longitudinal studies that characterize how the microbiome changes in response to estrogen are scarce. We aimed to compare the vaginal microbiota of postmenopausal women, before and 12 weeks after vaginal estrogen cream. Methods A total of 44 paired samples from 22 postmenopausal women with vaginal atrophy and stress incontinence were collected pre-vaginal estrogens and were compared to 12 weeks post-vaginal estrogen. Microbiota was characterized by 16S rRNA amplicon sequencing and biodiversity was investigated by comparing the alpha- and beta-diversity and potential markers were identified using differential abundance analysis. Results Vaginal estrogen treatment was associated with a reduction in vaginal pH and corresponded with a significant reduction in alpha diversity of the microbiota. Healthy vaginal community state type was associated with lower mean pH 4.89 (SD = 0.6), in contrast to dysbiotic state which had a higher mean pH 6.4 (SD = 0.74). Women with lactobacilli dominant community pre-treatment, showed stable microbiota and minimal change in their pH. Women with lactobacilli deficient microbiome pre-treatment improved markedly (p = 0.004) with decrease in pH -1.31 and change to heathier community state types. Conclusion In postmenopausal women with stress incontinence, vaginal estrogen promotes Lactobacillus and Bifidobacterium growth and lowers vaginal pH. Maximum response is seen in those with a dysbiotic vaginal microbiota pre-treatment.
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Affiliation(s)
- Kate H. Moore
- Department of Urogynaecology, St George Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Samantha Ognenovska
- Department of Urogynaecology, St George Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Xin-Yi Chua
- University of New South Wales Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Zhuoran Chen
- Department of Urogynaecology, St George Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Chloe Hicks
- University of New South Wales Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Fatima El-Assaad
- University of New South Wales Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Nevine te West
- Department of Urogynaecology, St George Hospital, University of New South Wales, Sydney, NSW, Australia
| | - Emad El-Omar
- University of New South Wales Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
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Strout N, Pasic L, Hicks C, Chua XY, Tashvighi N, Butler P, Liu Z, El-Assaad F, Holmes E, Susic D, Samaras K, Craig ME, Davis GK, Henry A, Ledger WL, El-Omar EM. The MothersBabies Study, an Australian Prospective Cohort Study Analyzing the Microbiome in the Preconception and Perinatal Period to Determine Risk of Adverse Pregnancy, Postpartum, and Child-Related Health Outcomes: Study Protocol. Int J Environ Res Public Health 2023; 20:6736. [PMID: 37754596 PMCID: PMC10531411 DOI: 10.3390/ijerph20186736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/03/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
The microbiome has emerged as a key determinant of human health and reproduction, with recent evidence suggesting a dysbiotic microbiome is implicated in adverse perinatal health outcomes. The existing research has been limited by the sample collection and timing, cohort design, sample design, and lack of data on the preconception microbiome. This prospective, longitudinal cohort study will recruit 2000 Australian women, in order to fully explore the role of the microbiome in the development of adverse perinatal outcomes. Participants are enrolled for a maximum of 7 years, from 1 year preconception, through to 5 years postpartum. Assessment occurs every three months until pregnancy occurs, then during Trimester 1 (5 + 0-12 + 6 weeks gestation), Trimester 2 (20 + 0-24 + 6 weeks gestation), Trimester 3 (32 + 0-36 + 6 weeks gestation), and postpartum at 1 week, 2 months, 6 months, and then annually from 1 to 5 years. At each assessment, maternal participants self-collect oral, skin, vaginal, urine, and stool samples. Oral, skin, urine, and stool samples will be collected from children. Blood samples will be obtained from maternal participants who can access a study collection center. The measurements taken will include anthropometric, blood pressure, heart rate, and serum hormonal and metabolic parameters. Validated self-report questionnaires will be administered to assess diet, physical activity, mental health, and child developmental milestones. Medications, medical, surgical, obstetric history, the impact of COVID-19, living environments, and pregnancy and child health outcomes will be recorded. Multiomic bioinformatic and statistical analyses will assess the association between participants who developed high-risk and low-risk pregnancies, adverse postnatal conditions, and/or childhood disease, and their microbiome for the different sample types.
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Affiliation(s)
- Naomi Strout
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
| | - Lana Pasic
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
| | - Chloe Hicks
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
| | - Xin-Yi Chua
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
| | - Niki Tashvighi
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
| | - Phoebe Butler
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
| | - Zhixin Liu
- UNSW Stats Central, Biological Sciences South Building (E26), Level 2 Kensington, UNSW Sydney, Sydney, NSW 2052, Australia
- Healthdirect Australia, Level 4, 477 Pitt Street, Sydney, NSW 2000, Australia
| | - Fatima El-Assaad
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
| | - Elaine Holmes
- The Australian National Phenome Centre, Harry Perkins Institute, Murdoch University, Perth, WA 6150, Australia;
| | - Daniella Susic
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
- Department of Women’s and Children’s Health, St George Hospital, Kogarah, NSW 2217, Australia; (G.K.D.); (A.H.)
- Discipline of Women’s Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW 2052, Australia; (M.E.C.); (W.L.L.)
| | - Katherine Samaras
- Complex Diseases Program, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia;
- Department of Endocrinology, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical Campus, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Maria E. Craig
- Discipline of Women’s Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW 2052, Australia; (M.E.C.); (W.L.L.)
| | - Gregory K. Davis
- Department of Women’s and Children’s Health, St George Hospital, Kogarah, NSW 2217, Australia; (G.K.D.); (A.H.)
- Discipline of Women’s Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW 2052, Australia; (M.E.C.); (W.L.L.)
| | - Amanda Henry
- Department of Women’s and Children’s Health, St George Hospital, Kogarah, NSW 2217, Australia; (G.K.D.); (A.H.)
- Discipline of Women’s Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW 2052, Australia; (M.E.C.); (W.L.L.)
| | - William L. Ledger
- Discipline of Women’s Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW 2052, Australia; (M.E.C.); (W.L.L.)
| | - Emad M. El-Omar
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW 2052, Australia; (N.S.); (L.P.); (C.H.); (X.-Y.C.); (F.E.-A.); (D.S.)
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Madders G, Becker L, Chua XY, Price G, Smith C, Gee E, Trafford A, Eisner D, Dibb K. A transcriptomic insight into the mechanism underlying the decrease in atrial ICa-L in heart failure. J Mol Cell Cardiol 2022. [DOI: 10.1016/j.yjmcc.2022.08.172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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O’Donnell M, Teasdale SB, Chua XY, Hardman J, Wu N, Curtis J, Samaras K, Bolton P, Morris MJ, Shannon Weickert C, Purves-Tyson T, El-Assaad F, Jiang XT, Hold GL, El-Omar E. The Role of the Microbiome in the Metabolic Health of People with Schizophrenia and Related Psychoses: Cross-Sectional and Pre-Post Lifestyle Intervention Analyses. Pathogens 2022; 11:1279. [PMID: 36365032 PMCID: PMC9695516 DOI: 10.3390/pathogens11111279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 03/20/2024] Open
Abstract
The microbiome has been implicated in the development of metabolic conditions which occur at high rates in people with schizophrenia and related psychoses. This exploratory proof-of-concept study aimed to: (i) characterize the gut microbiota in antipsychotic naïve or quasi-naïve people with first-episode psychosis, and people with established schizophrenia receiving clozapine therapy; (ii) test for microbiome changes following a lifestyle intervention which included diet and exercise education and physical activity. Participants were recruited from the Eastern Suburbs Mental Health Service, Sydney, Australia. Anthropometric, lifestyle and gut microbiota data were collected at baseline and following a 12-week lifestyle intervention. Stool samples underwent 16S rRNA sequencing to analyse microbiota diversity and composition. Seventeen people with established schizophrenia and five people with first-episode psychosis were recruited and matched with 22 age-sex, BMI and ethnicity matched controls from a concurrent study for baseline comparisons. There was no difference in α-diversity between groups at baseline, but microbial composition differed by 21 taxa between the established schizophrenia group and controls. In people with established illness pre-post comparison of α-diversity showed significant increases after the 12-week lifestyle intervention. This pilot study adds to the current literature that detail compositional differences in the gut microbiota of people with schizophrenia compared to those without mental illness and suggests that lifestyle interventions may increase gut microbial diversity in patients with established illness. These results show that microbiome studies are feasible in patients with established schizophrenia and larger studies are warranted to validate microbial signatures and understand the relevance of lifestyle change in the development of metabolic conditions in this population.
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Affiliation(s)
- Maryanne O’Donnell
- Discipline of Psychiatry and Mental Health, School of Medicine and Health, University of New South Wales, Kensington 2033, Australia
- Eastern Suburbs Mental Health Service, South Eastern Sydney Local Health District, Randwick 2031, Australia
| | - Scott B. Teasdale
- Discipline of Psychiatry and Mental Health, School of Medicine and Health, University of New South Wales, Kensington 2033, Australia
- Mindgardens Neuroscience Network, Sydney 2033, Australia
| | - Xin-Yi Chua
- Microbiome Research Centre, St George and Sutherland Clinical Campuses, University of New South Wales, Kogarah 2217, Australia
| | - Jamie Hardman
- Eastern Suburbs Mental Health Service, South Eastern Sydney Local Health District, Randwick 2031, Australia
| | - Nan Wu
- Microbiome Research Centre, St George and Sutherland Clinical Campuses, University of New South Wales, Kogarah 2217, Australia
- Department of Gastroenterology, The Sutherland Hospital, Caringbah 2229, Australia
| | - Jackie Curtis
- Discipline of Psychiatry and Mental Health, School of Medicine and Health, University of New South Wales, Kensington 2033, Australia
- Eastern Suburbs Mental Health Service, South Eastern Sydney Local Health District, Randwick 2031, Australia
- Mindgardens Neuroscience Network, Sydney 2033, Australia
| | - Katherine Samaras
- Department of Endocrinology, St Vincent’s Hospital Sydney, Victoria St, Darlinghurst 2010, Australia
- Clinical Obesity, Nutrition and Adipose Biology Lab, 384 Garvan Institute of Medical Research, Victoria St, Darlinghurst 2010, Australia
- School of Clinical Medicine, St Vincent’s Healthcare Clinical Campus, University of New South Wales, Darlinghurst 2010, Australia
| | - Patrick Bolton
- Eastern Suburbs Mental Health Service, South Eastern Sydney Local Health District, Randwick 2031, Australia
- School of Public Health, University of New South Wales, Kensington 2033, Australia
| | - Margaret J. Morris
- School of Medical Sciences, University of New South Wales, Kensington 2033, Australia
| | - Cyndi Shannon Weickert
- Discipline of Psychiatry and Mental Health, School of Medicine and Health, University of New South Wales, Kensington 2033, Australia
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney 2033, Australia
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, NY 13210, USA
| | - Tertia Purves-Tyson
- Discipline of Psychiatry and Mental Health, School of Medicine and Health, University of New South Wales, Kensington 2033, Australia
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney 2033, Australia
| | - Fatima El-Assaad
- Microbiome Research Centre, St George and Sutherland Clinical Campuses, University of New South Wales, Kogarah 2217, Australia
| | - Xiao-Tao Jiang
- Microbiome Research Centre, St George and Sutherland Clinical Campuses, University of New South Wales, Kogarah 2217, Australia
| | - Georgina L. Hold
- Microbiome Research Centre, St George and Sutherland Clinical Campuses, University of New South Wales, Kogarah 2217, Australia
| | - Emad El-Omar
- Microbiome Research Centre, St George and Sutherland Clinical Campuses, University of New South Wales, Kogarah 2217, Australia
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Appleyard SA, Maher S, Pogonoski JJ, Bent SJ, Chua XY, McGrath A. Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches. J Fish Biol 2021; 98:1421-1432. [PMID: 33484178 DOI: 10.1111/jfb.14687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Natural history collections are repositories of biodiversity and are potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic and forensic purposes. Specimens in fish collections are preserved using a combination of methods with many fixed in formalin and then preserved in ethanol for long-term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared the DNA barcoding and identification success for frozen and formalin-fixed tissues obtained from specimens in the CSIRO Australian National Fish Collection. They studied 230 samples from fishes (consisting of >160 fish species). An optimized formalin-fixed, paraffin-embedded DNA extraction method resulted in usable DNA from degraded tissues. Four mini barcoding assays of the mitochondrial DNA (mtDNA) were characterized with Sanger and Illumina amplicon sequencing. In the good quality DNA (without exposure to formalin), up to 88% of the specimens were correctly matched at the species level using the cytochrome oxidase subunit 1 (COI) mini barcodes, whereas up to 58% of the specimens exposed to formalin for less than 8 weeks were correctly identified to species. In contrast, 16S primers provided higher amplification success with formalin-exposed tissues, although the COI gene was more successful for identification. Importantly, the authors found that DNA of a certain size and quality can be amplified and sequenced despite exposure to formalin, and Illumina sequencing provided them with greater power of resolution for taxa identification even when there was little DNA present. Overall, within parameter constraints, this study highlights the possibilities of recovering DNA barcodes for identification from formalin-fixed fish specimens, and the authors provide guidelines for when successful identification could be expected.
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Affiliation(s)
- Sharon A Appleyard
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Safia Maher
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - John J Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections Australia, Hobart, Tasmania, Australia
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
| | - Stephen J Bent
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
| | - Xin-Yi Chua
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Annette McGrath
- CSIRO Environomics Future Science Platform, Canberra, Australian Capital Territory, Australia
- Data 61, CSIRO, Brisbane, Queensland, Australia
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Lovell DR, Chua XY, McGrath A. Counts: an outstanding challenge for log-ratio analysis of compositional data in the molecular biosciences. NAR Genom Bioinform 2020; 2:lqaa040. [PMID: 33575593 PMCID: PMC7671413 DOI: 10.1093/nargab/lqaa040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/08/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022] Open
Abstract
Thanks to sequencing technology, modern molecular bioscience datasets are often compositions of counts, e.g. counts of amplicons, mRNAs, etc. While there is growing appreciation that compositional data need special analysis and interpretation, less well understood is the discrete nature of these count compositions (or, as we call them, lattice compositions) and the impact this has on statistical analysis, particularly log-ratio analysis (LRA) of pairwise association. While LRA methods are scale-invariant, count compositional data are not; consequently, the conclusions we draw from LRA of lattice compositions depend on the scale of counts involved. We know that additive variation affects the relative abundance of small counts more than large counts; here we show that additive (quantization) variation comes from the discrete nature of count data itself, as well as (biological) variation in the system under study and (technical) variation from measurement and analysis processes. Variation due to quantization is inevitable, but its impact on conclusions depends on the underlying scale and distribution of counts. We illustrate the different distributions of real molecular bioscience data from different experimental settings to show why it is vital to understand the distributional characteristics of count data before applying and drawing conclusions from compositional data analysis methods.
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Affiliation(s)
| | - Xin-Yi Chua
- Queensland University of Technology, Australia
| | - Annette McGrath
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia
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Bernard G, Chan CX, Chan YB, Chua XY, Cong Y, Hogan JM, Maetschke SR, Ragan MA. Alignment-free inference of hierarchical and reticulate phylogenomic relationships. Brief Bioinform 2019; 20:426-435. [PMID: 28673025 PMCID: PMC6433738 DOI: 10.1093/bib/bbx067] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/04/2017] [Indexed: 11/22/2022] Open
Abstract
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA. Thus, next-generation phylogenomics must address computational scalability while rethinking the nature of orthogroups, the alignment of multiple sequences and the inference and comparison of trees. New phylogenomic workflows have begun to take shape based on so-called alignment-free (AF) approaches. Here, we review the conceptual foundations of AF phylogenetics for the hierarchical (vertical) and reticulate (lateral) components of genome evolution, focusing on methods based on k-mers. We reflect on what seems to be successful, and on where further development is needed.
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Abstract
Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.
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Affiliation(s)
- Mike W C Thang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4000, Australia.,Queensland Facility for Advanced Bioinformatics, University of Queensland, Brisbane, Queensland, 4000, Australia
| | - Xin-Yi Chua
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4000, Australia.,Queensland Facility for Advanced Bioinformatics, University of Queensland, Brisbane, Queensland, 4000, Australia
| | - Gareth Price
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4000, Australia.,Queensland Facility for Advanced Bioinformatics, University of Queensland, Brisbane, Queensland, 4000, Australia
| | - Dominique Gorse
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, 4000, Australia.,Queensland Facility for Advanced Bioinformatics, University of Queensland, Brisbane, Queensland, 4000, Australia
| | - Matt A Field
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Australian Institute for Tropical Health and Medicine, James Cook University, Smithfield, Queensland, 4878, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Smithfield, Queensland, 4878, Australia
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Abstract
OBJECTIVES Memory clinics play an important role in enabling early dementia diagnosis and intervention. Few studies have investigated the changing patient profiles at memory clinics over time. We studied the trend of patient characteristics in a geriatric medicine-led memory clinic over 12 years to improve services and care to meet their needs. SETTING AND PARTICIPANTS Data from 2340 first-visit patients seen at a memory clinic from 2005-2017 were extracted from a registered database and analysed. DESIGN ANOVA, Pearson chi-square and non-parametric tests were used to describe and compare between patients with dementia (PWD) and patients with no dementia (PND). MEASUREMENTS Data included diagnoses of dementia and mild cognitive impairment, age, education, MMSE scores and comorbidities. RESULTS Patients averaged 77.2 ± 8.3 years of age with mean MMSE score of 16.2 ± 6.7. Those diagnosed with dementia were older (78.3 ± 7.9 years) and almost half (48.4%) had moderate or moderately severe dementia (FAST 5-6). Over time, there was a growing proportion of patients with mild cognitive impairment (MCI) and mild Alzheimer's dementia. Many PWD had co-morbidities of hypertension (65.9%), hyperlipidemia (55.1%), diabetes (33.5%) and 28.4% were frail. CONCLUSIONS The findings call for services to better diagnose and manage patients at the earlier stages of cognitive impairment and provide holistic interventions for those with frailty and other co-morbidities. The continued rise in number of patients presenting to memory clinics provides impetus to expedite integration of tertiary-based memory clinics with primary and community care providers to better support PWD and their families.
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Affiliation(s)
- X Y Chua
- Philip Yap Lin Kiat, Affiliation: Khoo Teck Puat Hospital, Department of Geriatric Medicine, Singapore, 90 Yishun Central, Singapore 768828, , Tel: 65-66022154
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Gibb M, Chua XY, Gorse D, Queen D. The Australian wound registry. Aust Nurs Midwifery J 2015; 23:35. [PMID: 26665848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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