scholarly journals Comparative analysis of bacterial communities associated with healthy and diseased corals in the Indonesian sea

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8137 ◽  
Author(s):  
Wuttichai Mhuantong ◽  
Handung Nuryadi ◽  
Agus Trianto ◽  
Agus Sabdono ◽  
Sithichoke Tangphatsornruang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Coastal Development ◽  
Principal Coordinates Analysis ◽  
Bacterial Phyla ◽  
Principal Coordinates ◽  
White Band ◽  
Coral Reef Ecosystems ◽  
Black Band ◽  
White Band Disease ◽  
Pollutant Discharge

Coral reef ecosystems are impacted by climate change and human activities, such as increasing coastal development, overfishing, sewage and other pollutant discharge, and consequent eutrophication, which triggers increasing incidents of diseases and deterioration of corals worldwide. In this study, bacterial communities associated with four species of corals: Acropora aspera, Acropora formosa, Cyphastrea sp., and Isopora sp. in the healthy and disease stages with different diseases were compared using tagged 16S rRNA sequencing. In total, 59 bacterial phyla, 190 orders, and 307 genera were assigned in coral metagenomes where Proteobacteria and Firmicutes were pre-dominated followed by Bacteroidetes together with Actinobacteria, Fusobacteria, and Lentisphaerae as minor taxa. Principal Coordinates Analysis (PCoA) showed separated clustering of bacterial diversity in healthy and infected groups for individual coral species. Fusibacter was found as the major bacterial genus across all corals. The lower number of Fusibacter was found in A. aspera infected with white band disease and Isopora sp. with white plaque disease, but marked increases of Vibrio and Acrobacter, respectively, were observed. This was in contrast to A. formosa infected by a black band and Cyphastrea sp. infected by yellow blotch diseases which showed an increasing abundance of Fusibacter but a decrease in WH1-8 bacteria. Overall, infection was shown to result in disturbance in the complexity and structure of the associated bacterial microbiomes which can be relevant to the pathogenicity of the microbes associated with infected corals.

Calcified macroalgae and their bacterial community in relation to larval settlement and metamorphosis of reef-building coral Pocillopora damicornis

2020 ◽  
Vol 97 (1) ◽  
Author(s):  
Fangfang Yang ◽  
Jiahao Mo ◽  
Zhangliang Wei ◽  
Lijuan Long
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Larval Settlement ◽  
Pocillopora Damicornis ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Coral Reef Ecosystems ◽  
Settlement And Metamorphosis ◽  
Invertebrate Larvae

ABSTRACT Calcified macroalgae play an important role in the settlement and metamorphosis of invertebrate larvae in coral reef ecosystems. However, little is known about the algal-associated bacterial communities and their effects on larval settlement. In this study, the responses of larvae of the coral Pocillopora damicornis to calcified algae (Porolithon onkodes, Halimeda cylindracea, Halimeda opuntia and Amphiroa fragilissima) were evaluated. The results revealed that Por. onkodes and H. cylindracea significantly enhanced the rates of settlement and metamorphosis, whereas fewer larvae settled on Am. fragilissima and H. opuntia. Amplicon pyrosequencing of the V3–V4 region of 16S rDNA was applied to investigate the relationship between algal bacterial community and larval settlement. Principal coordinates analysis demonstrated that the bacterial community composition of H. opuntia was more similar to that of Am. fragilissima, but clearly distinct from those of H. cylindracea and Por. onkodes. Furthermore, the relative abundances of bacteria were highly diverse among different algae. H. opuntia had higher percentages of Thalassobius, Pelagibius and SM1A02, whereas the abundances of Mycoplasma and Suttonella were significantly higher in H. cylindracea than other algae. Our results showed that larval settlement/metamorphosis was strongly correlated with the bacterial community composition and with the relative abundance of a few operational taxonomic units.

scholarly journals Changes in the gut bacterial communities in colon cancer surgery patients: an observational study

Gut Pathogens ◽  
2022 ◽  
Vol 14 (1) ◽  
Author(s):  
Mohamed Abbas ◽  
Nadia Gaïa ◽  
Nicolas C. Buchs ◽  
Vaihere Delaune ◽  
Myriam Girard ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Bacterial Communities ◽  
Antimicrobial Prophylaxis ◽  
Colon Surgery ◽  
Cancer Surgery ◽  
Gene Marker ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Colon Cancer Surgery

Abstract Background Colon surgery has been shown to modulate the intestinal microbiota. Our objective was to characterize these changes using state-of-the-art next generation sequencing techniques. Methods We performed a single-centre prospective observational cohort study to evaluate the changes in the gut microbiota, i.e., taxon distribution, before and after elective oncologic colon surgery in adult patients with different antimicrobial prophylaxis regimens (standard prophylaxis with cefuroxime/metronidazole versus carbapenems for extended-spectrum beta-lactamase-producing Enterobacterales [ESBL-E] carriers). We obtained rectal samples on the day of surgery, intraoperative luminal samples, and rectal or stoma samples 3 days after surgery. We performed metataxonomic analysis based on sequencing of the bacterial 16S rRNA gene marker. Similarities and differences between bacterial communities were assessed using Bray–Curtis similarity, visualised using principal coordinates analysis and statistically tested by PERMANOVA. Comparison of taxa relative abundance was performed using ANCOM. Results We included 27 patients between March 27, 2019 and September 17, 2019. The median age was 63.6 years (IQR 56.4–76.3) and 44% were females. Most (81%) patients received standard perioperative prophylaxis as they were not ESBL carriers. There was no significant association between ESBL carriage and differences in gut microbiome. We observed large and significant increases in the genus Enterococcus between the preoperative/intraoperative samples and the postoperative sample, mainly driven by Enterococcus faecalis. There were significant differences in the postoperative microbiome between patients who received standard prophylaxis and carbapenems, specifically in the family Erysipelotrichaceae. Conclusion This hypothesis-generating study showed rapid changes in the rectal microbiota following colon cancer surgery.

PREVALENSI DAN KELIMPAHAN PENYAKIT KARANG DI PERAIRAN DESA BUTON KABUPATEN MOROWALI SULAWESI TENGAH

2021 ◽  
Vol 6 (1) ◽  
pp. 1
Author(s):  
Ayu Safitri ◽  
Ratna Diyah Palupi ◽  
. Rahmadani
Keyword(s):  
White Spot ◽  
Black Band Disease ◽  
White Band ◽  
Brown Band ◽  
Black Band ◽  
Belt Transect ◽  
White Band Disease ◽  
Brown Band Disease

Penyakit karang sekarang ini sudah menjadi perhatian utama para peneliti karang. Banyak kasus dilaporkan penyakit karang menjadi penyumbang terbesar kematian karang di sebuah perairan. Penelitian ini bertujuan untuk mengetahui prevalensi dan kelimpahan penyakit karang di Perairan Desa Buton, Kabupaten Morowali, Sulawesi Tengah. Metode pengambilan data prevalensi dan kelimpahan penyakit karang menggunkan belt transect (transek sabuk) dengan luas 180m2 yang ditarik sejajar garis pantai pada 3 (tiga) titik stasiun. Hasil penelitian menunjukan ditemukan sebanyak 5 (lima) jenis penyakit karang (White Band Disease, Brown Band Disease, Ulcerative White Spot, Bleaching, dan Black Band Disease dan 3 (tiga) jenis gangguan kesehatan karang (Fish bites, Crown-of-Thorn-Starfish (COTS), dan Tube formers). Secara umum total prevalensi penyakit karang di lokasi penelitian sebesar 78,7% (52,3% penyakit karang dan 26,4% berupa gangguan kesehatan karang) dengan kasus tertinggi terdapat di stasiun 1 (satu). lebih lanjut kelimpahan rata-rata penyakit karang sebesar 0,65 koloni/m2. Kelimpahan penyakit karang tertinggi ditemukan pada stasiun I yaitu sebesar 0,32 koloni/m2.Kata Kunci: Penyakit Karang, Prevalensi, Kelimpahan, Perairan Desa Buton

scholarly journals KELIMPAHAN DAN PREVALENSI PENYAKIT KARANG DI PERAIRAN LANGARA, KONAWA KEPULAUAN, SULAWESI TENGGARA

2019 ◽  
Vol 4 (2) ◽  
pp. 99
Author(s):  
Siti Hasma ◽  
Baru Sadarun ◽  
Ratna Diyah Palupi
Keyword(s):  
Black Band Disease ◽  
Yellow Band ◽  
Growth Anomalies ◽  
White Spots ◽  
White Band ◽  
Black Band ◽  
Belt Transect ◽  
Yellow Band Disease ◽  
White Band Disease

Penyakit karang adalah gangguan terhadap kesehatan karang yang menyebabkan hilang atau rusaknya jaringan karang. Biota karang yang terinfeksi penyakit telah diidentifikasikan sebagai salah satu faktor utama yang memperburuk tutupan terumbu karang secara global. Tujuan dari penelitian ini untuk mengetahui kelimpahan dan prevalensi penyakit karang di Perairan Langara, Konawe Kepulauan, Sulawesi Tenggara. Pengambilan data dilakukan di bulan April 2018 pada tiga stasiun penelitian. Metode pengambilan data kelimpahan dan prevalensi penyakit karang menggunakan metode belt transect (transek sabuk) dengan luas area transek 350 m2, yang ditarik sejajar garis pantai. Hasil penelitian menyebutkan bahwa penyakit karang yang ditemukan di lokasi penelitian sebanyak 8 jenis [Black Band Disease (BBD), Dark Spots Disease (DSD), Ulcerative White Spots (UWS), White Band Disease (WBD), Explained Growth Anomalies (EGA), White Syndrom (WS), Bleacing (BL) dan Yellow Band Disease (YBD)]. Kelimpahan dan prevalensi penyakit karang yang tertinggi terdapat di stasiun II, dimana nilai kelimpahan yaitu 0.063 koloni/m2 dan nilai prevalensi yaitu 92.187%. Jenis penyakit karang yang mendominasi di lokasi penelitian secara berturut-turut adalah UWS, BBD dan WS.Kata Kunci: Kelimpahan; Penyakit Karang; Perairan Langara; Prevalensi

scholarly journals Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1803
Author(s):  
Valentino Palombo ◽  
Elena De Zio ◽  
Giovanna Salvatore ◽  
Stefano Esposito ◽  
Nicolaia Iaffaldano ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Fishery Management ◽  
Snp Array ◽  
Fine Scale ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Management Actions ◽  
Principal Coordinates ◽  
Mediterranean Trout

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

scholarly journals Tree Species Diversity and Composition of Miombo Woodlands in South-Central Angola: A Chronosequence of Forest Recovery after Shifting Cultivation

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Francisco M. P. Gonçalves ◽  
Rasmus Revermann ◽  
Amândio L. Gomes ◽  
Marcos P. M. Aidar ◽  
Manfred Finckh ◽  
...  
Keyword(s):  
Shifting Cultivation ◽  
Stand Structure ◽  
Woody Species ◽  
Distinct Group ◽  
Forest Recovery ◽  
Miombo Woodlands ◽  
Principal Coordinates Analysis ◽  
South Central ◽  
Principal Coordinates ◽  
Management Plans

The study was carried out in the Cusseque area of the Municipality of Chitembo in south-central Angola. Our objectives were to assess the floristic diversity, the species composition, and stand structure of Miombo woodlands during regeneration after shifting cultivation. A total of 40 plots of 1000 m2were surveyed and analyzed, corresponding to mature forests/woodlands and three fallow types of different age. The analyses were based on plot inventories of all trees with DBH ≥ 5 cm. A total of 51 woody species, 38 genera, and 19 families were recorded. The dominant family was Fabaceae, with subfamily Caesalpinioideae being very abundant. Shannon Diversity and Evenness were highest in mature forests and young fallows, while the mature forest stands showed the highest species richness. A Principal Coordinates Analysis (PCoA) showed many species shared between the intermediate fallow types, but only few species were shared with young fallows. Mature forests formed a clearly distinct group. This study shows potential pathways of forest recovery in terms of faster regeneration after agricultural abandonment and, thus, the results presented here can be used in future conservation and management plans in order to reduce the pressure on mature forests.

scholarly journals Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Runzhi Zhang ◽  
Alejandro R. Walker ◽  
Susmita Datta
Keyword(s):  
Machine Learning ◽  
Error Rates ◽  
Average Error ◽  
Importance Score ◽  
Learning Methods ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Total Variability ◽  
The Common ◽  
Feature Selecting

Abstract Background Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB “Forensic Challenge”. The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets. Results Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as “mystery” samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common “family”, “order” of the main-dataset and the common “order” of the mystery dataset provided the most efficient information for prediction respectively. Conclusions The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.

Genetic analysis of a heritage variety collection

2018 ◽  
Vol 17 (03) ◽  
pp. 232-244 ◽  
Author(s):  
J. M. Preston ◽  
B. V. Ford-Lloyd ◽  
L. M. J. Smith ◽  
R. Sherman ◽  
N. Munro ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Group Method ◽  
Niche Markets ◽  
Principal Coordinates Analysis ◽  
Pair Group ◽  
Landrace Diversity ◽  
Principal Coordinates ◽  
Length Polymorphisms ◽  
Seed Saving ◽  
History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”

2014 ◽  
Vol 92 (2) ◽  
pp. 149-162 ◽  
Author(s):  
Christina M. Davy ◽  
Robert W. Murphy
Keyword(s):  
Population Genetics ◽  
Freshwater Turtles ◽  
Population Declines ◽  
Isolated Populations ◽  
Principal Coordinates Analysis ◽  
Turtle Species ◽  
Principal Coordinates ◽  
Clemmys Guttata ◽  
Spotted Turtle ◽  
Cast Doubt

Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.

Use of multivariate methods in forest research site selection

1991 ◽  
Vol 21 (11) ◽  
pp. 1573-1580 ◽  
Author(s):  
Andrew J. Burton ◽  
Carl W. Ramm ◽  
Kurt S. Pregitzer ◽  
David D. Reed
Keyword(s):  
Site Selection ◽  
Large Scale ◽  
Multivariate Methods ◽  
Data Bases ◽  
Principal Coordinates Analysis ◽  
Research Site ◽  
Principal Coordinates ◽  
Alternative Sites ◽  
Existing Data ◽  
Selection Of

In large-scale gradient studies, selection of the best research sites is critical but time-consuming and costly. Multivariate methods can be used to quickly identify suitable sites from existing data bases. Based on a study of acid deposition in the Great Lakes region (the Michigan Gradient Study), we illustrate the use of multivariate methods in screening potential research sites for similarity. Sites were examined using cluster analysis, principal coordinates analysis, and correspondence analysis. The graphical displays generated by the multivariate methods were used to identify similar sites across the gradient. A list of 31 potential sites was reduced to 5 similar research sites and several alternative sites. The results of the multivariate methods compared well with more traditional methods of research site selection but allowed for multiple comparisons of many potential sites using a variety of data from existing data bases. By eliminating sites that are unacceptable with respect to available data, the multivariate methods reduce the number of sites that require field visitation prior to final site verification. This process represents a substantial savings in time and effort when dealing with a long list of potential research sites.

Sign in / Sign up

Export Citation Format

Share Document