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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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Point pattern analysis as a tool for assessing disease spread and population features in remaining sanctuaries of the critically endangered bivalve Pinna nobilis. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Guo R, Xu X, Sun Z, Hu X. Performance and bacterial community of bio-electrochemical system treating simulated domestic wastewater containing low concentration of cephalosporin antibiotics. ENVIRONMENTAL TECHNOLOGY 2022; 43:893-906. [PMID: 32807023 DOI: 10.1080/09593330.2020.1811390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
This study investigated the effects of five cephalosporin antibiotics (ceftazidime, ceftriaxone, cefdinir, cefixime and cefepime) on performance and bacterial community structure in bio-electrochemical systems (BES) and sequencing batch biofilm reactor (SBBR). The results showed that the external electric field had no significant effect on the removal of COD and ammonia nitrogen in water. The removal rates of five antibiotics in BES increased by 28.5%, 20.0%, 9.1%, 21.0%, and 11.5%, respectively. High-through sequencing showed that microbial membrane-growing process increased species diversity, and antibiotics had a significant inhibitory effect on the initial biofilm of the reactor. As time progressed, the inhibitory effect was weakened, and the microorganism were tolerated and re-enriched. The increase in the type and concentration of antibiotics and the applied electric field had a significant effect on the microorganisms in the reactor. The dominant microorganisms for antibiotic removal in the SBBR were Luteococcus, Cloacibacterium, Dysgonomonas, and Ottowia. The dominant bacteria in the BES were Ottowia and Tahibacte. The abundance of these strains increased significantly during antibiotic acclimation. The abundance of Ottowia, Tahibacter, and Nakamurella were significantly higher than SBBR. Thus the BES system had a good antibiotic degradation effect. The BES can effectively treat simulated domestic sewage containing multiple antibiotics, laying a theoretical foundation for the actual wastewater treatment.
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Affiliation(s)
- Ruijie Guo
- Research Group of Water Pollution Control and Water Reclamation, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Xin Xu
- Research Group of Water Pollution Control and Water Reclamation, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
| | - Zhirong Sun
- College of Environmental & Energy Engineering, Beijing University of Technology, Beijing, People's Republic of China
| | - Xiang Hu
- Research Group of Water Pollution Control and Water Reclamation, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, People's Republic of China
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Simas AM, Kramer CD, Genco CA. Diet-Induced Non-alcoholic Fatty Liver Disease and Associated Gut Dysbiosis Are Exacerbated by Oral Infection. FRONTIERS IN ORAL HEALTH 2022; 2:784448. [PMID: 35141703 PMCID: PMC8820505 DOI: 10.3389/froh.2021.784448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Increasing evidence indicates that chronic inflammation due to periodontal disease is associated with progression of non-alcoholic fatty liver disease (NAFLD) caused by a Western diet. NAFLD has also been associated with oral infection with the etiological agent of periodontal disease, Porphyromonas gingivalis. P. gingivalis oral infection has been shown to induce cardiometabolic disease features including hepatic lipid accumulation while also leading to dysbiosis of the gut microbiome. However, the impact of P. gingivalis infection on the gut microbiota of mice with diet-induced NAFLD and the potential for those changes to mediate NAFLD progression has yet to be determined. In the current study, we have demonstrated that P. gingivalis infection induced sustained alterations of the gut microbiota composition and predicted functions, which was associated with the promotion of NAFLD in steatotic mice. Reduced abundance of short-chain fatty acid-producing microbiota was observed after both acute and chronic P. gingivalis infection. Collectively, our findings demonstrate that P. gingivalis infection produces a persistent change in the gut microbiota composition and predicted functions that promotes steatosis and metabolic disease.
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Affiliation(s)
- Alexandra M. Simas
- Gerald J. and Dorothy R. Friedman School of Nutrition and Science Policy, Graduate Program in Biochemical and Molecular Nutrition, Tufts University, Boston, MA, United States
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
| | - Carolyn D. Kramer
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
| | - Caroline A. Genco
- Department of Immunology, Tufts University School of Medicine, Boston, MA, United States
- Graduate Program in Immunology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, United States
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, United States
- *Correspondence: Caroline A. Genco
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Schang K, Cox K, Trant AJ. Habitation Sites Influence Tree Community Assemblages in the Great Bear Rainforest, British Columbia, Canada. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.791047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Identifying how past human actions have influenced their environment is essential for understanding the ecological factors that structure contemporary ecosystems. Intertidal resource use by Indigenous Peoples for thousands of years has led to habitation sites containing vast shell midden deposits and facilitating long-term impacts on soil chemistry and drainage. Here we examine how these shell middens have impacted various forest metrics, such as species diversity, community composition, canopy height, and regeneration recruitment to determine if forests on habitation sites differ from the surrounding matrix. We surveyed known habitation sites with archeological evidence indicating past year-round human occupation, within the Hakai Lúxvbálís Conservancy on Calvert and Hecate Islands within the Great Bear Rainforest along British Columbia’s Central Coast. Our results demonstrate that habitation sites exhibit lower tree species richness, less relative species abundances, as such, displayed lower Shannon diversity and inverse Simpson values. The composition of tree communities on habitation sites was statistically different, with western hemlock and western redcedar densities increasing on non-habitation sites. Conversely, regeneration diversity at habitation sites was more even and exhibited elevated Shannon diversity and inverse Simpson values. The community composition of regeneration was more consistent among habitation and non-habitation sites; however, western redcedar, western hemlock and Sitka spruce were more abundant at habitation sites. For all tree species, maximum height was higher within the habitation sites; however, this trend was the most notable in western redcedar and Sitka spruce, which increased by an average of 4.8 m relative to non-habitation sites. Collectively, our findings suggest that long-term habitation alters forest community compositions. The landscape alterations within habitation sites promote conditions needed to support diverse, even, and abundant regeneration communities and consequently increase the height of the dominant coastal tree species. Thus, our results offer evidence that long-term influence by Indigenous communities have a persistent influence on coastal forests.
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Tiwari G, Pandey P, Kaul R, Lee H, Singh R. Comparison of point and roadside transect methods to evaluate the abundance and richness of diurnal raptors in the arid region of Rajasthan. PLoS One 2021; 16:e0259805. [PMID: 34879090 PMCID: PMC8654222 DOI: 10.1371/journal.pone.0259805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022] Open
Abstract
Diurnal raptors show a wider distribution compared to other groups of birds including passerines, woodpeckers, and seriemas, but occur at lower-than-expected densities. Estimating the precise abundance is essential to achieve conservation goals but the methods used to estimate the populations of birds need to be appropriate to arrive at meaningful conclusions. We compared the two survey methods: roadside point count and strip transects, for estimating species richness and abundance of raptors in the arid landscape of Rajasthan. Roadside point counts and roadside strip transects were done on 50 transects between December 2019- February 2020 (with an average length of 20 km and a total distance of 3000 km) to assess the species richness and abundance of raptors. A total of 2954 observations of raptors belonging to 35 species were recorded using both methods. Mann Whitney U test result showed no significant difference in species richness and abundance estimates between both methods (p = 0.206). The point count method yielded a higher relative abundance of 2.79 individuals [10 km2]-1h-1 than the 1.90 individuals [10 km2]-1h-1 obtained during the strip transect. Also, the number of unidentified species were less for point counts. Extrapolation values indicated that both the methods do not differ much for the detection of unsampled species. The choice of survey method depends on the objectives of the study, but our results favor the use of point counts rather than strip transects to survey raptors in open habitats. The information generated from this study is expected to provide the most efficient method to study the abundance and distribution of raptors in similar landscapes.
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Affiliation(s)
- Govind Tiwari
- Amity Institute of Forestry and Wildlife, Amity University, Noida, Uttar Pradesh, India
| | - Puneet Pandey
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- * E-mail: (PP); (HL); (RS)
| | - Rahul Kaul
- Wildlife Trust of India, Noida, Uttar Pradesh, India
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
- * E-mail: (PP); (HL); (RS)
| | - Randeep Singh
- Amity Institute of Forestry and Wildlife, Amity University, Noida, Uttar Pradesh, India
- * E-mail: (PP); (HL); (RS)
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Barnes RSK. What does measuring species diversity in estuarine seagrass systems actually assess? MARINE ENVIRONMENTAL RESEARCH 2021; 172:105500. [PMID: 34653926 DOI: 10.1016/j.marenvres.2021.105500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/01/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
Relationships between species diversity and other species-density and species-richness metrics were investigated in the seagrass macrobenthos of Knysna estuarine bay, South Africa. Although a wide range of species density occurred across sites, neither Hill-Shannon nor Hill-Simpson diversity showed any significant relationship with it, although they did with species richness. Instead species diversity was very closely related to relative evenness, and (negatively) to overall assemblage abundance. No significant relationship was found between species density and evenness. Whilst there was a clear and marked decrease in species density upstream along the main estuarine channel, only one of the species-diversity indices (the Hill-Shannon) showed a significant equivalent decrease. Relationships depended on how 'species richness' was assessed, and were very strongly influenced by the superabundant local occurrence of a few individual faunal components (three gastropod and one tanaid species). Species-diversity analysis contributes nothing new in such estuarine seagrass meadows and seems best avoided.
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Affiliation(s)
- R S K Barnes
- Department of Zoology and Entomology, Rhodes University, Makhanda, Eastern Cape, 6140, South Africa; Department of Zoology & Conservation Research Institute, University of Cambridge, Cambridge, UK.
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Reconciling resource extraction and species conservation in a multi-use landscape: Immediate and long-term impacts of logging on rainforest mammal diversity. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Affiliation(s)
- Michael Roswell
- Graduate Program in Ecology and Evolution, Rutgers Univ. New Brunswick NJ USA
- Dept of Entomology, Univ. of Maryland College Park College Park MD USA
| | - Jonathan Dushoff
- Dept of Ecology, Evolution and Natural Resources, Rutgers Univ. New Brunswick NJ USA
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Abstract
The Mekong River is one of the world’s largest rivers and has an annual captured fish production of about 2.3 million tonnes, equivalent to around 11 billion USD. Although the Mekong provides important ecological and socioeconomic benefits to millions of people, it is facing intensive change due to anthropogenic stressors. Therefore, it is necessary to understand the changes to the spatiotemporal fish communities to inform sustainable fisheries management. Here, we aimed to characterize patterns of the fish communities and identify the ecological status of each fish community using daily catch data from 2007 to 2018 at 25 monitoring sites in the Lower Mekong Basin (LMB). The collected data were classified by a self-organizing map into four main groups. Group 4 represented the lower Vietnam Mekong Delta (VMD), while groups 1, 2, and 3 were subdivided into subgroups 1a (upper LMB), 1b (upper and middle LMB), 2a (Mekong River below the Khone Falls and Sesan River), 2b (Mekong River below the Khone Falls and Sekong, Sesan and Srepok (3S) Rivers), 3a (Floodplain-Tonle Sap and Songkhram) and 3b (upper VMD). Among the 571 species recorded, 119 were identified as indicator species. Based on the abundance and biomass comparison curves, the fish community of 2b was in a healthier condition with a positive W-statistic value while the rest had a negative W-statistic value. The highest species richness and diversity were observed in 3a and 2b, so these subgroups deserve high management and conservation priority. Likewise, 1a should also be considered as a high priority area since it harbors several endangered and long-distant migratory fishes. It was also noticed that the fish communities of groups 3 and 4, located far from the hydropower dams, remained mostly unchanged compared to those of groups 1 and 2, close to the mainstream and tributary dams in the upper LMB and 3S Rivers.
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Campbell L, Dudas SE, Juanes F, Allen Gerwing AM, Gerwing TG. Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada. J NAT HIST 2020. [DOI: 10.1080/00222933.2020.1770886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lily Campbell
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Sarah E. Dudas
- Department of Biology, Vancouver Island University, Nanaimo, British Columbia, Canada
- Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Francis Juanes
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | | | - Travis G. Gerwing
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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Chakraborty J, Sapkale V, Rajput V, Shah M, Kamble S, Dharne M. Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 194:110443. [PMID: 32155479 DOI: 10.1016/j.ecoenv.2020.110443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Anthropogenic activities mediated antibiotic resistance genes (ARGs) in the pristine aquatic bodies (lakes) is raising concern worldwide. Long read shotgun sequencing was used to assess taxonomic diversity, distribution of ARGs and metal resistance genes (MRGs) and mobile genetic elements (MGEs) in six sites within hypersaline Lonar soda lake (India) prone to various anthropogenic activities. Proteobacteria and Euryarchaeota were dominant phyla under domain Bacteria and Archaea respectively. Higher abundance of Bacteroidetes was pragmatic at sites 18LN5 and 18LN6. Functional analysis indicated 26 broad-spectrum ARGs types, not reported earlier in this ecosystem. Abundant ARG types identified were multidrug efflux, glycopepetide, bacitracin, tetracycline and aminogylcoside resistance. Sites 18LN1 and 18LN5 depicted 167 and 160 different ARGs subtypes respectively and rpoB2, bcrA, tetA(48), mupA, ompR, patA, vanR and multidrug ABC transporter genes were present in all samples. The rpoB2 gene was dominant in 18LN1, whereas bcrA gene in 18LN2-18LN6 sites. Around 24 MRGs types were detected with higher abundance of arsenic in 18LN1 and copper in 18LN2-18LN6, signifying metal contamination linked to MRGs. The bacterial taxa Pseudomonas, Thioalkalivibrio, Burkholderia, Clostridium, Paenibacillus, Bacillus and Streptomyces were significantly associated with ARGs. This study highlights the resistomic hotspots in the lake for deploying policies for conservation efforts.
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Affiliation(s)
- Jaya Chakraborty
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Vibhavari Sapkale
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Manan Shah
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Sanjay Kamble
- Chemical Engineering and Process Development (CEPD) Division, CSIR-National Chemical Laboratory (NCL), Pune, India
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), CSIR-National Chemical Laboratory (NCL), Pune, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Abstract
Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depends on the context and application, and whether a predictive mechanistic model exists. In this topical review, we first summarize the relevant mathematical principles underlying heterogeneity in a large population, before outlining the various definitions of 'diversity' and providing examples of scientific topics in which its quantification plays an important role. We then review how diversity has been a ubiquitous concept across multiple fields, including ecology, immunology, cellular barcoding experiments, and socioeconomic studies. Since many of these applications involve sampling of populations, we also review how diversity in small samples is related to the diversity in the entire population. Features that arise in each of these applications are highlighted.
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Affiliation(s)
- Song Xu
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, United States of America
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Leite GGS, Morales W, Weitsman S, Celly S, Parodi G, Mathur R, Sedighi R, Barlow GM, Rezaie A, Pimentel M. Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study. BMC Microbiol 2019; 19:239. [PMID: 31675917 PMCID: PMC6824053 DOI: 10.1186/s12866-019-1617-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 10/20/2019] [Indexed: 12/16/2022] Open
Abstract
Background The human small intestine plays a central role in the processes of digestion and nutrient absorption. However, characterizations of the human gut microbiome have largely relied on stool samples, and the associated methodologies are ill-suited for the viscosity and low microbial biomass of small intestine samples. As part of the REIMAGINE study to examine the specific roles of the small bowel microbiome in human health and disease, this study aimed to develop and validate methodologies to optimize microbial analysis of the small intestine. Results Subjects undergoing esophagogastroduodenoscopy without colon preparation for standard of care were prospectively recruited, and ~ 2 ml samples of luminal fluid were obtained from the duodenum using a custom sterile aspiration catheter. Samples of duodenal aspirates were either untreated (DA-U, N = 127) or pretreated with dithiothreitol (DA-DTT, N = 101), then cultured on MacConkey agar for quantitation of aerobic gram-negative bacteria, typically from the class Gammaproteobacteria, and on blood agar for quantitation of anaerobic microorganisms. DA-DTT exhibited 2.86-fold greater anaerobic bacterial counts compared to DA-U (P = 0.0101), but were not statistically different on MacConkey agar. DNA isolation from DA-U (N = 112) and DA-DTT (N = 43) samples and library preparation for 16S rRNA gene sequencing were also performed using modified protocols. DA-DTT samples exhibited 3.81-fold higher DNA concentrations (P = 0.0014) and 4.18-fold higher 16S library concentrations (P < 0.0001) then DA-U samples. 16S rRNA gene sequencing revealed increases in the detected relative abundances of obligate and facultative anaerobes in DA-DTT samples, including increases in the genera Clostridium (false discovery rate (FDR) P = 4.38E-6), Enterococcus (FDR P = 2.57E-8), Fusobacterium (FDR P = 0.02) and Bacteroides (FDR P = 5.43E-9). Detected levels of Gram-negative enteropathogens from the phylum Proteobacteria, such as Klebsiella (FDR P = 2.73E-6) and Providencia (FDR P < 0.0001) (family Enterobacteriaceae) and Pseudomonas (family Pseudomonadaceae) (FDR P = 0.04), were also increased in DA-DTT samples. Conclusions This study validates novel DTT-based methodology which optimizes microbial culture and 16S rRNA gene sequencing for the study of the small bowel microbiome. The microbial analyses indicate increased isolation of facultative and obligate anaerobes from the mucus layer using these novel techniques.
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Affiliation(s)
| | - Walter Morales
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stacy Weitsman
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shreya Celly
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gonzalo Parodi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ruchi Mathur
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rashin Sedighi
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gillian M Barlow
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ali Rezaie
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Pimentel
- Medically Associated Science and Technology (MAST) Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA. .,Division of Digestive and Liver Diseases, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Relationships between Potentially Toxic Elements in intertidal sediments and their bioaccumulation by benthic invertebrates. PLoS One 2019; 14:e0216767. [PMID: 31536494 PMCID: PMC6752810 DOI: 10.1371/journal.pone.0216767] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/05/2019] [Indexed: 11/19/2022] Open
Abstract
The bioaccumulation of Potentially Toxic Elements (PTEs) by benthic invertebrates in estuarine sediments is poorly understood. We sampled and analysed PTEs in sediments and benthic invertebrates from five sites in the Skeena Estuary (British Columbia, Canada), including sites adjacent to an abandoned cannery and a decommissioned papermill. Our aim was to elucidate baseline levels of PTE concentrations at sites that may be recovering from disturbance associated with prior industrial development and identify organisms that could be used to biomonitor the impact of future industrial developments. There was no indication that sediments of the salmon cannery were polluted, but acidic sediments adjacent to the papermill contained elevated concentrations of Cd, Cr, Hg and Pb. Benthic invertebrate community assemblages confirm that sediments have mostly recovered from prior industrial development associated with discharge of papermill sludge. Overall, we did not observe any relationship between PTE concentrations in the sediment and PTE concentrations in invertebrate tissues. However, we did observe a negative relationship between sediment pH and the Biota-Sediment Accumulation Factor (BSAF) of most PTEs for Oregon pill bugs (Gnorimosphaeroma oregonensis). G. oregonensis, observed at all sites, feeds on the fibers associated with the papermill discharge. Thus, G. oregonensis is a useful biomonitors for quantifying the impact of the decommissioned papermill, and are candidate biomonitors for assessing the impact of similar industrial development projects on intertidal ecosystems.
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Sha SP, Suryavanshi MV, Tamang JP. Mycobiome Diversity in Traditionally Prepared Starters for Alcoholic Beverages in India by High-Throughput Sequencing Method. Front Microbiol 2019; 10:348. [PMID: 30891011 PMCID: PMC6411702 DOI: 10.3389/fmicb.2019.00348] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
Chowan, dawdim, humao, hamei, khekhrii, and phut are sun-dried starters used for preparation of alcoholic beverages in North East regions of India. We attempted to profile the mycobiome community in these starters by high-throughput sequencing (HTS) method. All fungal populations were found to be restricted to Ascomycota (67-99%), Zygomycota (0.7-29%), Basidiomycota (0.03-7%), and Chytridiomycota (0.0003%). We found 45 core operational taxonomic units (OTUs) which were universally present and were further weighed to 41 genera level and 22 species level taxonomy. A total number of 594 fungal species were detected by HTS including common species (224), unique species (133) and rare-species (237) in samples of starters. Unique species were recorded in phut (40 species), khekhrii (28), hamei (23), dawdim (21), chowan (13), and humao (8), respectively. Most of the fungal families were found to correlate to a type of nutritional mode and growth morphologies of the community, where saprotrophic mode of mold species were more dominant, whereas morphotypes were more dominant in yeast species.
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Affiliation(s)
| | | | - Jyoti Prakash Tamang
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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Gerwing TG, Campbell L, Allen Gerwing AM, Allen S, Cox K, Rogers M, Gray O, Drewes M, Juanes F. Potential impacts of logging on intertidal infaunal communities within the Kitimat River estuary. J NAT HIST 2019. [DOI: 10.1080/00222933.2018.1553249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Affiliation(s)
- Travis G. Gerwing
- Ecosystem Science and Management Program, University of Northern British Columbia, British Columbia, Canada
- Department of Biology, University of Victoria, Victoria, Canada
- LGL Environmental Research Associates, Sidney, Canada
| | - Lily Campbell
- Department of Biology, University of Victoria, Victoria, Canada
| | - Alyssa M. Allen Gerwing
- Ecosystem Science and Management Program, University of Northern British Columbia, British Columbia, Canada
| | - Shaun Allen
- Ecosystem Science and Management Program, University of Northern British Columbia, British Columbia, Canada
| | - Kieran Cox
- Department of Biology, University of Victoria, Victoria, Canada
| | - Megan Rogers
- Hidden River Environmental Management, Terrace, Canada
| | - Olivia Gray
- Hidden River Environmental Management, Terrace, Canada
| | - Mitch Drewes
- Hidden River Environmental Management, Terrace, Canada
| | - Francis Juanes
- Department of Biology, University of Victoria, Victoria, Canada
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18
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Cox KD, Black MJ, Filip N, Miller MR, Mohns K, Mortimor J, Freitas TR, Greiter Loerzer R, Gerwing TG, Juanes F, Dudas SE. Community assessment techniques and the implications for rarefaction and extrapolation with Hill numbers. Ecol Evol 2017; 7:11213-11226. [PMID: 29299294 PMCID: PMC5743490 DOI: 10.1002/ece3.3580] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/13/2017] [Accepted: 09/16/2017] [Indexed: 11/06/2022] Open
Abstract
Diversity estimates play a key role in ecological assessments. Species richness and abundance are commonly used to generate complex diversity indices that are dependent on the quality of these estimates. As such, there is a long-standing interest in the development of monitoring techniques, their ability to adequately assess species diversity, and the implications for generated indices. To determine the ability of substratum community assessment methods to capture species diversity, we evaluated four methods: photo quadrat, point intercept, random subsampling, and full quadrat assessments. Species density, abundance, richness, Shannon diversity, and Simpson diversity were then calculated for each method. We then conducted a method validation at a subset of locations to serve as an indication for how well each method captured the totality of the diversity present. Density, richness, Shannon diversity, and Simpson diversity estimates varied between methods, despite assessments occurring at the same locations, with photo quadrats detecting the lowest estimates and full quadrat assessments the highest. Abundance estimates were consistent among methods. Sample-based rarefaction and extrapolation curves indicated that differences between Hill numbers (richness, Shannon diversity, and Simpson diversity) were significant in the majority of cases, and coverage-based rarefaction and extrapolation curves confirmed that these dissimilarities were due to differences between the methods, not the sample completeness. Method validation highlighted the inability of the tested methods to capture the totality of the diversity present, while further supporting the notion of extrapolating abundances. Our results highlight the need for consistency across research methods, the advantages of utilizing multiple diversity indices, and potential concerns and considerations when comparing data from multiple sources.
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Affiliation(s)
- Kieran D Cox
- Hakai Institute Calvert Island BC Canada.,Department of Biology University of Victoria Victoria BC Canada.,Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada
| | - Morgan J Black
- Hakai Institute Calvert Island BC Canada.,Department of Biology University of Victoria Victoria BC Canada.,Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada
| | - Natalia Filip
- Hakai Institute Calvert Island BC Canada.,Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada
| | - Matthew R Miller
- Hakai Institute Calvert Island BC Canada.,Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada
| | - Kayla Mohns
- Hakai Institute Calvert Island BC Canada.,Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada
| | - James Mortimor
- Pacific Region Pacific Biological Station Fisheries and Oceans Canada Nanaimo BC Canada
| | - Thaise R Freitas
- Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada.,Centro de Estudos do Mar Universidade Federal do Paraná Pontal do Paraná Paraná Brazil
| | - Raquel Greiter Loerzer
- Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada
| | - Travis G Gerwing
- Hakai Institute Calvert Island BC Canada.,Ecosystem Science and Management Program University of Northern British Columbia Prince George BC Canada
| | - Francis Juanes
- Department of Biology University of Victoria Victoria BC Canada
| | - Sarah E Dudas
- Hakai Institute Calvert Island BC Canada.,Department of Biology University of Victoria Victoria BC Canada.,Department of Biology Centre for Shellfish Research Vancouver Island University Nanaimo BC Canada
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