scholarly journals First dynamics of bacterial community during development of Acropora humilis larvae in aquaculture

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chitrasak Kullapanich ◽  
Suppakarn Jandang ◽  
Matanee Palasuk ◽  
Voranop Viyakarn ◽  
Suchana Chavanich ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Population ◽  
Antibiotic Production ◽  
16S Rrna Gene Sequencing ◽  
Cell Development ◽  
Rrna Gene ◽  
Round Cell ◽  
Cell Stage ◽  
Embryonic Cleavage ◽  
Population Structures

AbstractA symbiosis of bacterial community (sometimes called microbiota) play essential roles in developmental life cycle and health of coral, starting since a larva. For examples, coral bacterial holobionts function nitrogen fixation, carbon supply, sulfur cycling and antibiotic production. Yet, a study of the dynamic of bacteria associated coral larvae development is complicated owning to a vast diversity and culturable difficulty of bacteria; hence this type of study remains unexplored for Acropora humilis larvae in Thai sea. This study represented the first to utilize 16S rRNA gene sequencing to describe the timely bacterial compositions during successfully cultured and reared A. humilis larval transformation in aquaculture (gametes were collected from Sattahip Bay, Chonburi province, Thailand), from gamete spawning (0 h) and fertilization stage (1 h), to embryonic cleavage (8 h), round cell development (28, 39 and 41 h), and planula formation (48 h). The sequencing results as estimated by Good’s coverage at genus level covered 99.65 ± 0.24% of total bacteria. While core phyla of bacteria were observed (Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes), changes in bacterial population structures and differential predominant core bacterial orders were denoted for each larval developmental stage, from fertilization to embryonic cleavage and subsequently from the embryonic cleavage to round cell development (P = 0.007). For instances, Pseudoalteromonas and Oceanospirillales were found prevalent at 8 h, and Rhizobiales were at 48 h. The bacterial population structures from the round cell stage, particularly at 41 h, showed gradual drift towards those of the planula formation stage, suggesting microbial selection. Overall, this study provides preliminary insights into the dynamics of bacterial community and their potentially functional association (estimated from the bacterial compositions) during the developmental embryonic A. humilis in a cultivation system in Southeast Asia region.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

scholarly journals The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot

2020 ◽  
Vol 98 (7) ◽  
Author(s):  
Christina B Welch ◽  
Jeferson M Lourenco ◽  
Dylan B Davis ◽  
Taylor R Krause ◽  
Mia N Carmichael ◽  
...  
Keyword(s):  
Feed Efficiency ◽  
Bacterial Population ◽  
Diversity Index ◽  
16S Rrna Gene Sequencing ◽  
Nutrient Utilization ◽  
Rrna Gene ◽  
Feedlot Steers ◽  
Taxonomic Profile ◽  
Bacterial Richness ◽  
The Impact

Abstract Feed is the greatest cost of animal production, so reducing it is critical to increase producer profits. In ruminants, the microbial population within the gastrointestinal tract (GIT) is critical to nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the bacterial taxonomic profile of the rumen, cecum, and feces of feedlot steers at slaughter in order to link feed efficiency and the GIT bacterial populations from these three locations. Twenty commercial Angus steers were selected and divided into two groups according to their residual feed intake (RFI) classification determined during the feedlot-finishing period: high-RFI (n = 10) and low-RFI (n = 10). After the ruminal, cecal, and fecal samples were collected at slaughter, DNA extraction and 16S rRNA gene sequencing were performed on them to determine their bacterial composition. One-way ANOVA was performed on the animal performance data, alpha diversities, and bacterial abundances using RFI classification as the fixed effect. Overall, the ruminal bacterial population was the most different in terms of taxonomic profile compared with the cecal and fecal populations as revealed by beta diversity analysis (P < 0.001). Moreover, bacterial richness (Chao1) was greatest (P = 0.01) in the rumen of the high-RFI group compared with the low-RFI group. In contrast, bacterial richness and diversity in the intestinal environment showed that Chao1 was greater (P = 0.01) in the cecum, and the Shannon diversity index was greater in both the cecum and feces of low-RFI compared with high-RFI steers (P = 0.01 and P < 0.001, respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P = 0.01); fecal Bifidobacteriaceae was more abundant in high-RFI steers (P = 0.03). No correlations (P ≥ 0.13) between any ruminal bacterial family and RFI were detected; however, Ruminococcaceae, Mogibacteriaceae, Christensenellaceae, and BS11 were negatively correlated with RFI (P < 0.05) in the cecum and feces. Succinivibrionaceae in the cecum was positively correlated with RFI (P = 0.05), and fecal Bifidobacteriaceae was positively correlated with RFI (P = 0.03). Results collectively indicate that in addition to the ruminal bacteria, the lower gut bacterial population has a significant impact on feed efficiency and nutrient utilization in feedlot steers; therefore, the intestinal bacteria should also be considered when examining the basis of ruminant feed efficiency.

scholarly journals Distinctly different bacterial communities in surface and oxygen minimum layers in the Arabian Sea

2016 ◽  
Author(s):  
Mandar Bandekar ◽  
Nagappa Ramaiah ◽  
Anand Jain ◽  
Ram Murti Meena
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Arabian Sea ◽  
16S Rrna Gene Sequencing ◽  
Molecular Techniques ◽  
Rrna Gene ◽  
Northeast Monsoon ◽  
Rrna Gene Sequencing ◽  
Oxygen Minimum

Abstract. Contributions of microbial communities to biogeochemical processes in oxygen minimum oceanic zones are being realized through the applications of molecular techniques. To understand seasonal and depth-wise variations in bacterial community structure (BCS) in the Arabian Sea oxygen minimum region, extensive sampling and molecular analyses were carried out. 16S rRNA gene sequencing was done to profile the BCS from five depths, surface (5 m), deep chorophyll maximum (43–50 m, DCM), 250 m, 500 m and 1000 m during Spring intermonsoon (SIM), Fall intermonsoon (FIM), and Northeast monsoon (NEM) seasons. Sequencing of 743 chimera-free clones revealed a clear vertical partitioning of BCS between the surface (surface + DCM) and OMZ (250 + 500 + 1000 m) layers. There was no distinct seasonal difference in the BCS. Most 16S rRNA gene sequences were affiliated to Gammaproteobacteria (39.31 %), Alphaproteobacteria (23.56 %) and Cyanobacteria (20.2 %). Higher diversity and OTUs in OMZ predominantly consisting of Alteromonodales, Sphinogomonadales, Rhodobacterales, Burkholderales, and Acidimicrobiales we observed might be due to their microaerophilic metabolism, ability to degrade recalcitrant substrates and assimilate sinking particulate matter. Further hitherto undescribed diversity both in surface and OMZ layers was evidenced. Implicit role of extant bacterial community in denitrification and anammox and in sulphur oxidation is highlighted.

scholarly journals Sex Results in Divergence in Gut Bacterial Community between Female and Male Pardosa astrigera (Araneae: Lycosidae)

2021 ◽  
Author(s):  
Ying Gao ◽  
Pengfeng Wu ◽  
Shuyan Cui ◽  
Abid Ali ◽  
Guo Zheng
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
Relative Abundance ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Factors Affecting ◽  
Β Diversity ◽  
Pardosa Astrigera ◽  
Rrna Gene Sequencing ◽  
Agro Forestry

Sex is one of the important factors affecting gut microbiota. As key predators in agro-forestry ecosystem, many spider species show dramatically different activity habits and nutritional requirements between female and male. However, how sex affects gut microbiota of spiders is still unclear. Therefore, in this study, the compositions and diversities of gut bacteria, based on bacterial 16S rRNA gene sequencing, were compared between female and male Pardosa astrigera. We found that bacterial richness indices (P < 0.05) in female were significantly lower than male, meanwhile, β-diversity showed significantly different between female and male (P < 0.05). The relative abundance of Actinobacteriota and Rhodococcus (belongs to Actinobacteria) were significantly higher in female than male (P < 0.05). Whereas, the relative abundance of Firmicutes and Acinetobacter (belongs to Proteobacteria), Ruminococcus and Fusicatenibacter (all belong to Firmicutes), were significantly higher in male than female (P < 0.05). The results of PICRUSt2 showed that amino acid and lipid metabolisms were significantly higher in female than male (P < 0.05), whereas glycan biosynthesis and metabolism was significantly higher in male than female (P < 0.05). Our results imply that sexual variation is a crucial factor in shaping gut bacterial community in P. astrigera. Male P. astrigera dispersed more widely than the female hence the male had a higher bacterial diversity. While the distinct differences of bacterial composition mainly due to their different nutritional and energy requirements.

scholarly journals Fluoride contributes to the shaping of microbial community in high fluoride groundwater in Qiji County, Yuncheng City, China

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xin Zhang ◽  
Xubo Gao ◽  
Chengcheng Li ◽  
Xuesong Luo ◽  
Yanxin Wang
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Community Composition ◽  
Fluoride Concentration ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbial Response ◽  
Groundwater Samples ◽  
Groundwater Systems ◽  
Rrna Gene Sequencing

Abstract As a toxic element, excessive amounts of fluoride in environment can be harmful because of its antimicrobial activity, however little is known about the relationship between fluoride and the bacterial community in groundwater systems. Here, we use samples from a typical fluorosis area to test the hypothesis that fluoride concentration is a fundamental structuring factor for bacterial communities in groundwater. Thirteen groundwater samples were collected; high-throughput 16S rRNA gene sequencing and statistical analysis were conducted to compare the bacterial community composition in individual wells. The results showed that Proteobacteria, with most relative abundance in groundwater, decreased along the groundwater fluoride concentration. Additionally, relative abundances of 12 families were also statistically correlated with fluoride concentration. The bacterial community was significantly explained by TOC (P = 0.045) and fluoride concentration (P = 0.007) of groundwater. This suggests that fluoride and TOC likely plays an important role in shaping the microbial community structure in these groundwater systems. Our research suggest that fluoride concentration should be taken into consideration in future when evaluating microbial response to environmental conditions in groundwater system, especially for fluoride rich groundwater.

scholarly journals Manipulating the banana rhizosphere microbiome for biological control of Panama disease

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Chao Xue ◽  
C. Ryan Penton ◽  
Zongzhuan Shen ◽  
Ruifu Zhang ◽  
Qiwei Huang ◽  
...  
Keyword(s):  
Biological Control ◽  
Microbial Community ◽  
Bacterial Community ◽  
Disease Incidence ◽  
16S Rrna Gene Sequencing ◽  
Control Agent ◽  
Rrna Gene ◽  
Panama Disease ◽  
Suppressive Soil ◽  
Pathogen Colonization

Abstract Panama disease caused by Fusarium oxysporum f. sp. cubense infection on banana is devastating banana plantations worldwide. Biological control has been proposed to suppress Panama disease, though the stability and survival of bio-control microorganisms in field setting is largely unknown. In order to develop a bio-control strategy for this disease, 16S rRNA gene sequencing was used to assess the microbial community of a disease-suppressive soil. Bacillus was identified as the dominant bacterial group in the suppressive soil. For this reason, B. amyloliquefaciens NJN-6 isolated from the suppressive soil was selected as a potential bio-control agent. A bioorganic fertilizer (BIO), formulated by combining this isolate with compost, was applied in nursery pots to assess the bio-control of Panama disease. Results showed that BIO significantly decreased disease incidence by 68.5%, resulting in a doubled yield. Moreover, bacterial community structure was significantly correlated to disease incidence and yield and Bacillus colonization was negatively correlated with pathogen abundance and disease incidence, but positively correlated to yield. In total, the application of BIO altered the rhizo-bacterial community by establishing beneficial strains that dominated the microbial community and decreased pathogen colonization in the banana rhizosphere, which plays an important role in the management of Panama disease.

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