Differential abundance and core members of the bacterial community associated with wild male Zeugodacus cucurbitae fruit flies (Insecta: Tephritidae) from three geographical regions of Southeast Asia

2019 ◽  
Vol 46 (4) ◽  
pp. 3765-3776 ◽  
Author(s):  
Hoi-Sen Yong ◽  
Sze-Looi Song ◽  
Praphathip Eamsobhana ◽  
Anchana Pasartvit ◽  
Phaik-Eem Lim
Keyword(s):  
Bacterial Community ◽  
Southeast Asia ◽  
Fruit Flies ◽  
Differential Abundance ◽  
Wild Male ◽  
Geographical Regions

Comparative Analysis of the Gut Bacterial Community of Four Anastrepha Fruit Flies (Diptera: Tephritidae) Based on Pyrosequencing

2018 ◽  
Vol 75 (8) ◽  
pp. 966-976 ◽  
Author(s):  
Carmen Ventura ◽  
Carlos I. Briones-Roblero ◽  
Emilio Hernández ◽  
Flor N. Rivera-Orduña ◽  
Gerardo Zúñiga
Keyword(s):  
Comparative Analysis ◽  
Bacterial Community ◽  
Fruit Flies

scholarly journals Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline

2022 ◽  
Vol 194 (2) ◽  
Author(s):  
Maria Grazia Bonomo ◽  
Luana Calabrone ◽  
Laura Scrano ◽  
Sabino Aurelio Bufo ◽  
Katia Di Tomaso ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Crude Oil ◽  
Soil Bacterial Community ◽  
Differential Abundance ◽  
Naturally Occurring ◽  
Basilicata Region ◽  
The Family ◽  
Soil Bacterial ◽  
Differential Abundance Analysis ◽  
Bacterial Groups

AbstractThis study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (− 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between − 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between − 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between − 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between − 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.

scholarly journals Genomic epidemiology of artemisinin resistant malaria

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Keyword(s):  
Southeast Asia ◽  
Selective Sweep ◽  
Low Frequency ◽  
Artemisinin Resistance ◽  
Synonymous Mutations ◽  
Genomic Epidemiology ◽  
Geographical Regions ◽  
Great Excess ◽  
Deep Reservoir ◽  
Practical Implications

The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.

scholarly journals Genetic variation in a radish (Raphanus sativus L.) geodiversity collection

2021 ◽  
Author(s):  
J. Arro ◽  
J. A. Labate
Keyword(s):  
North America ◽  
Southeast Asia ◽  
Central Asia ◽  
Allelic Variation ◽  
Genetic Relationships ◽  
East Asian ◽  
Germplasm Conservation ◽  
Southeast Asian ◽  
Gene Pools ◽  
Geographical Regions

AbstractA radish panel of 152 accessions with diverse root shapes was assembled from the National Plant Germplasm System (NPGS) collection based on weighted geographical sampling. Accessions represented 35 countries and were categorized into eight geographical regions—North America, Europe, Africa, West Asia, Central Asia, South Asia, East Asia, and Southeast Asia. Multiple plants per accession were assayed using genotyping by sequencing (GBS), and 8539 high-quality polymorphisms were discovered. Average observed heterozygosity (Ho) of the markers consistently ranged from 5 to 7% in all geographical regions. Central Asia was most diverse in terms of average expected heterozygosity (He = 0.107), while Southeast Asia was the least diverse (He = 0.050). Europe and Southeast Asia were the most divergent from each other (pairwise FST = 0.199), while Europe and North America were the least divergent (pairwise FST = 0.022). The clustering of genotypes based on principal components analysis (PCA) illustrated an east/west geographical pattern. Large numbers of private alleles and a substantial proportion (3%) of markers showing signals of selection based on allele frequency differences indicate that allelic variation is available for cultivar development. European and North American gene pools could be expanded by crossing with East Asian and Southeast Asian germplasm, and vice-versa. Both could potentially benefit from South Asian sources, while the addition of West Asian germplasm could increase East Asian and Southeast Asian diversity. This resource for molecular marker development combined with an understanding of global genetic relationships will inform the continued germplasm conservation and genetic improvement of radish.

Dynamics of bacterial community in Tonle Sap Lake, a large tropical flood-pulse system in Southeast Asia

2019 ◽  
Vol 664 ◽  
pp. 414-423 ◽  
Author(s):  
Porsry Ung ◽  
Chanthol Peng ◽  
Sokunsreiroat Yuk ◽  
Reasmey Tan ◽  
Vannak Ann ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Southeast Asia ◽  
Flood Pulse ◽  
Pulse System ◽  
Tonle Sap Lake ◽  
Tonle Sap

scholarly journals Metadata Analysis For Gut Microbiota between Indoor and Street Cats of Malaysia

2021 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
HAJAR FAUZAN AHMAD ◽  
Darren Dean Tay ◽  
Shing Wei Siew ◽  
Mohd Najib Razali
Keyword(s):  
Bacterial Community ◽  
Genomic Dna ◽  
Alpha Diversity ◽  
Complex Nature ◽  
Microbiota Composition ◽  
Sequencing Technology ◽  
Bacterial Composition ◽  
Differential Abundance ◽  
Metadata Analysis ◽  
Stool Samples

With the advancement of sequencing technology, the studies related to the complex nature of microbial communities are possible to be untapped. The goal of this study is to perform a comparison between the composition of bacteria between the gut of Malaysian indoor and street cats. For this research, stool samples of the cats were collected where the genomic DNA were extracted using DNeasy PowerSoil Pro Kit. The extracted DNA were sequenced by targeting the bacterial community using primers from V4 region of 16S rRNA. The raw data were analysed using QIIME2 to obtain the diversity, taxonomy, and differential abundance between the groups. Here, we found that indoor and street cats have similar alpha diversity (p > 0.05), with slight differences between the groups based on the bacterial composition. Likewise, the beta diversity suggest that the two groups are similar to each other. The genus Bifidobacterium, Clostridium, Collinsella, Enterococcus, Cantenibacterium and Lactobacillus from phylum Firmicutes while were found to be more abundant in indoor cats while street cats had more of the phylum Actinobacteria from the genus of  Acinetobacter, Blautia, and Olsenella. Hence, we observed whether a cat is kept indoor or is a stray does not significantly cause a shift in their respective microbiota composition.

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