Molecular characterization and structure of intestinal micro flora for postmortem interval estimation in SD rats

2019 ◽  
Author(s):  
Huan Li ◽  
Lu Yuan ◽  
Ruina Liu ◽  
Siruo Zhang ◽  
E Yang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Interval Estimation ◽  
Pcr Amplification ◽  
Postmortem Interval ◽  
The Body ◽  
Rrna Gene ◽  
Variable Regions ◽  
Time Points ◽  
Almost All

Abstract Background The human rectum flora consists of a huge variety of bacteria and the association between individuals and their rectum bacterial community begins presently after birth and continues the whole lifetime. Once the body dies, the inherent microbes begin to break down from the inside and play a key role thereafter. Results The aim of this study was to investigate the probable shift of the rectum flora at different time intervals up to 15 days after death and to characterize the contribution for of this shift to estimate the time of death. The rectum of rats was wiped with a sterile cotton swab and the samples were proceeded for DNA extraction, PCR amplification of the 16S rRNA gene with the V3+V4 variable regions, and high throughput sequencing carried out on IonS5TMXL platform. The results were analyzed for intra-group and inter-group diversity, similarity and difference at different time points. At phylum level, Proteobacteria and Firmicutes showed major shifts, checked at 11 different intervals and emerged in the most of postmortem intervals. At the genus level, Enterococcus appeared in all groups except alive samples, Lactobacillus and Proteus appeared in most time points, and the latter showed an increasing trend after 3 days postmortem samples. At the species level, Enterococcus_faecalis and Proteus_mirabilis existed in most postmortem intervals, and the former had a downward trend after day 5 postmortem, while the latter had an upward trend. Corynebacterium_amycolatum , Entero_isolate_group_2 , Bacteroides_uniformis , Enterococcus_faecalis , Streptococcus_gallolyticus_subsp_macedonics , Clostridium_sporogenes were more abundant in 0-hour, day 1, 3, 5, 7, 13 postmortem intervals, respectively, while Proteus_mirabilis and Vagococcus_lutrae were abundant in day 15 postmortem. In addition, functional capacity analysis of Membrane_Transport, Amino_Acid_Metabolism, Nucleotide_Metabolism and Energy_Metabolism showed significant differences between alive and almost all other time points after death ( P <0.05). Conclusions All in all, bacteria at different levels (phylum, genera, species) showed different characteristic during the process of decomposition and possessed entirely different relative abundance and the structure of bacterial community in each time point shifted obviously, which suggested that the specific bacteria might imply the specific postmortem interval during decomposition.

Potential Using of Molecular Characterization and Structure of The Gut Bacterial Community for Postmortem Interval Estimation in Sprague Dawley Rats

2020 ◽  
Author(s):  
Huan Li ◽  
Siruo Zhang ◽  
Ruina Liu ◽  
Lu Yuan ◽  
Di Wu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Interval Estimation ◽  
The Body ◽  
Time Of Death ◽  
Sprague Dawley ◽  
Upward Trend ◽  
Time Intervals ◽  
Taxa Richness ◽  
Sprague Dawley Rats

Abstract Once the body dies, the inherent microbes of the host begin to break down from the inside and play a key role thereafter. It is hypothesized that after the death certain rectal microbes would change during the decomposition course in the body. This study aimed to investigate the probable shift in the composition of the rectal flora at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time of death. At the phylum level, Proteobacteria and Firmicutes showed major shifts, when checked at 11 different intervals, and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis existed at most postmortem intervals; the former showed a downward trend after day 5 postmortem, while the latter showed an upward trend. There were obvious differences in bacterial community structure and richness at the phylum, genus, and species levels during the decomposition of the corpse of rats. The phylum, genus, and species taxa richness decreased initially and then increased significantly. The turning point came on day 9 when genus, rather than phylum or species, contained the most information for estimating the time of death. We constructed a prediction model using genus taxon data from high-throughput sequencing, which explained 87.2% of the time since the first sampling within 1 h. Seven bacteria, namely Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The above-mentioned bacteria showed a promising future for estimating the shortest time of death and results of current study were agreeing with the proposed hypothesis.

scholarly journals Potential use of molecular and structural characterization of the gut bacterial community for postmortem interval estimation in Sprague Dawley rats

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huan Li ◽  
Siruo Zhang ◽  
Ruina Liu ◽  
Lu Yuan ◽  
Di Wu ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Interval Estimation ◽  
The Body ◽  
Taxon Richness ◽  
Time Since Death ◽  
Sprague Dawley ◽  
Sprague Dawley Rats ◽  
Level Data ◽  
Species Taxon

AbstractOnce the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.

scholarly journals Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Matteo Daghio ◽  
Francesca Ciucci ◽  
Arianna Buccioni ◽  
Alice Cappucci ◽  
Laura Casarosa ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Performance ◽  
Community Composition ◽  
Lipid Composition ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Daily Weight Gain ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

Analysis of the effects of nanosilver on bacterial community in the intestinal fluid of silkworms using high-throughput sequencing

2019 ◽  
Vol 110 (3) ◽  
pp. 309-320
Author(s):  
Chen Lin ◽  
Zhou Wei ◽  
Zhou Yi ◽  
Tan Tingting ◽  
Du Huamao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Intestinal Bacteria ◽  
Illumina Miseq ◽  
The Body ◽  
Dependent Manner ◽  
Negative Effects ◽  
Silkworm Larvae ◽  
Intestinal Bacterial Community

AbstractNanosilver is an environment-friendly, harmless alternative of traditional disinfectants which can be potentially applied in the sericulture industry. However, the effects of nanosilver on the intestinal bacterial community of the silkworms (Bombyx mori L.) are unclear. In this study, Illumina MiSeq high-throughput sequencing technology was used to assess the intestinal bacterial community in both male and female silkworms while treated with different concentrations of nanosilver. We found that nanosilver significantly influenced the composition of silkworm intestinal bacterial community on the different taxonomic levels. Most conspicuously, the abundance of Firmicutes was increased by the treatment of 20 mg L−1 nanosilver but decreased by that of 100 mg L−1 nanosilver at the phylum level. The same trend was observed in Bacilli at the class level and in Enterococcus at the genus level. In some extreme cases, application of nanosilver eliminated the bacterium, e.g., Brevibacillus, but increased the population of several other bacteria in the host intestine, such as Blautia, Terrisporobacter, Faecalibacterium, and some bacteria could only be found in nanosilver treatment groups, e.g., Dialister. In addition, although nanosilver generally showed negative effects on the cocooning rate in a dose-dependent manner, we found that 20 mg L−1 nanosilver treatment significantly increased the body weight of silkworms and did not show negative effects on the survival rate. These results indicated that the intestinal bacteria community of silkworm larvae was significantly changed after nanosilver treatment which might consequently influence host growth and development.

scholarly journals Rice SST Variation Shapes the Rhizosphere Bacterial Community, Conferring Tolerance to Salt Stress through Regulating Soil Metabolites

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Tengxiang Lian ◽  
Yingyong Huang ◽  
Xianan Xie ◽  
Xing Huo ◽  
Muhammad Qasim Shahid ◽  
...  
Keyword(s):  
Salt Stress ◽  
Bacterial Community ◽  
Management Practices ◽  
High Throughput Sequencing ◽  
Crop Productivity ◽  
Soil Salinization ◽  
Rrna Gene ◽  
Content Type ◽  
Rice Mutant ◽  
Rhizosphere Bacterial Community

ABSTRACT Some plant-specific resistance genes could affect rhizosphere microorganisms by regulating the release of root exudates. In a previous study, the SST (seedling salt tolerant) gene in rice (Oryza sativa) was identified, and loss of SST function resulted in better plant adaptation to salt stress. However, whether the rice SST variation could alleviate salt stress via regulating soil metabolites and microbiota in the rhizosphere is still unknown. Here, we used transgenic plants with SST edited in the Huanghuazhan (HHZ) and Zhonghua 11 (ZH11) cultivars by the CRISPR/Cas9 system and found that loss of SST function increased the accumulation of potassium and reduced the accumulation of sodium ions in rice plants. Using 16S rRNA gene amplicon high-throughput sequencing, we found that the mutant material shifted the rhizobacterial assembly under salt-free stress. Importantly, under salt stress, the sst, HHZcas, and ZH11cas plants significantly changed the assembly of the rhizobacteria. Furthermore, the rice SST gene also affected the soil metabolites, which were closely related to the dynamics of rhizosphere microbial communities, and we further determined the relationship between the rhizosphere microbiota and soil metabolites. Overall, our results show the effects of the rice SST gene on the response to salt stress associated with the soil microbiota and metabolites in the rhizosphere. This study reveals a helpful linkage among the rice SST gene, soil metabolites, and rhizobacterial community assembly and also provides a theoretical basis for improving crop adaptation through soil microbial management practices. IMPORTANCE Soil salinization is one of the major environmental stresses limiting crop productivity. Crops in agricultural ecosystems have developed various strategies to adapt to salt stress. We used rice mutant and CRISPR-edited lines to investigate the relationships among the Squamosa promoter Binding Protein box (SBP box) family gene (SST/OsSPL10), soil metabolites, and the rhizosphere bacterial community. We found that during salt stress, there are significant differences in the rhizosphere bacterial community and soil metabolites between the plants with the SST gene and those without it. Our findings provide a useful paradigm for revealing the roles of key genes of plants in shaping rhizosphere microbiomes and their relationships with soil metabolites and offer new insights into strategies to enhance rice tolerance to high salt levels from microbial and ecological perspectives.

scholarly journals Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1055 ◽  
Author(s):  
Arturo Levican ◽  
Jenny C. Fisher ◽  
Sandra L. McLellan ◽  
Ruben Avendaño-Herrera
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Native Species ◽  
High Throughput Sequencing ◽  
Disease Outbreaks ◽  
Emerging Pathogens ◽  
Prophylactic Measures ◽  
Almost All ◽  
Conger Eel ◽  
Genypterus Chilensis

The red conger eel (Genypterus chilensis, Guichenot) is a native species included in the Chilean Aquaculture Diversification Program due to high commercial demand. In the context of intensified farming, prior reports link two disease outbreaks with emerging pathogens in the Vibrio and Tenacibaculum genera. However, the roles remain unclear for the bacterial community and each specific bacterium is associated with the rearing environment for healthy specimens. The success of red conger eel farming therefore warrants research into the bacterial composition of aquaculture conditions and the antimicrobial susceptibilities thereof. This study used culturing methods and high-throughput sequencing to describe the bacterial community associated with water in which G. chilensis was farmed. With culturing methods, the predominant genera were Vibrio (21.6%), Pseudolteromonas (15.7%), Aliivibrio (13.7%), and Shewanella (7.8%). Only a few bacterial isolates showed amylase, gelatinase, or lipase activity, and almost all showed inhibition zones to commonly-used antibiotics in aquaculture. By contrast, high-throughput sequencing established Paraperlucidibaca, Colwellia, Polaribacter, Saprospiraceae, and Tenacibaculum as the predominant genera, with Vibrio ranking twenty-seventh in abundance. High-throughput sequencing also established a link between previous outbreaks with increased relative abundances of Vibrio and Tenacibaculum. Therefore, monitoring the presence and abundance of these potential pathogens could be useful in providing prophylactic measures to prevent future outbreaks.

scholarly journals Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

2015 ◽  
Vol 81 (20) ◽  
pp. 7067-7077 ◽  
Author(s):  
W. Ahmed ◽  
C. Staley ◽  
M. J. Sadowsky ◽  
P. Gyawali ◽  
J. P. S. Sidhu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Fecal Pollution ◽  
Rrna Gene ◽  
Potential Sources

ABSTRACTIn this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways.

scholarly journals Bacterial Community Structure and Diversity in a Century-Old Manure-Treated Agroecosystem

2004 ◽  
Vol 70 (10) ◽  
pp. 5868-5874 ◽  
Author(s):  
H. Y. Sun ◽  
S. P. Deng ◽  
W. R. Raun
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Management Practices ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Lime Treatment ◽  
Soil Microbial Community Structure ◽  
Treated Soil

ABSTRACT Changes in soil microbial community structure and diversity may reflect environmental impact. We examined 16S rRNA gene fingerprints of bacterial communities in six agroecosystems by PCR amplification and denaturing gradient gel electrophoresis (PCR-DGGE) separation. These soils were treated with manure for over a century or different fertilizers for over 70 years. Bacterial community structure and diversity were affected by soil management practices, as evidenced by changes in the PCR-DGGE banding patterns. Bacterial community structure in the manure-treated soil was more closely related to the structure in the untreated soil than that in soils treated with inorganic fertilizers. Lime treatment had little effect on bacterial community structure. Soils treated with P and N-P had bacterial community structures more closely related to each other than to those of soils given other treatments. Among the soils tested, a significantly higher number of bacterial ribotypes and a more even distribution of the bacterial community existed in the manure-treated soil. Of the 99 clones obtained from the soil treated with manure for over a century, two (both Pseudomonas spp.) exhibited 100% similarity to sequences in the GenBank database. Two of the clones were possible chimeras. Based on similarity matching, the remaining 97 clones formed six major clusters. Fifty-six out of 97 were assigned taxonomic units which grouped into five major taxa: α-, β-, and γ-Proteobacteria (36 clones), Acidobacteria (16 clones), Bacteroidetes (2 clones), Nitrospirae (1 clone), and Firmicutes (1 clone). Forty-one clones remained unclassified. Results from this study suggested that bacterial community structure was closely related to agroecosystem management practices conducted for over 70 years.

scholarly journals Putative functions and co-occurrence patterns of the microbial communities in natural and engineered ecosystems

2021 ◽  
Author(s):  
Yu Xia ◽  
Na Li ◽  
Yiyun Chen ◽  
Weijia Li ◽  
Xuwen He ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Rrna Gene ◽  
Natural Environments ◽  
Anaerobic Digesters ◽  
Network Analyses ◽  
Wb Network ◽  
Almost All ◽  
Occurrence Patterns

Abstract Understanding functions and co-occurrence patterns of microbial communities in various ecosystems enriches the knowledge on ecosystem characteristics and microbial ecology. However, such analyses have rarely been reported. Herein, functions and inter-taxa correlations of microbial communities in a set of natural environments (farmland (SA), forest soil (SB) and Caspian Sea sediments (CSS)) and engineered ecosystems (wastewater treatment plants (FW, WA and WB) and anaerobic digesters (AD)) were studied based on FAPROTAX and network analyses, respectively, by a collection of 115 samples from seven published 16S rRNA gene datasets generated by high-throughput sequencing. The results show that chemoheterotrophy related populations were the most abundant in almost all the communities. Their relative abundances (RAs) in the AD systems were the highest (43.7%±4.2%), followed by those of the soil environments (40.2%±1.9% in SA and 36.4%±2.0% in SB). For each ecosystem, the indicative community and overall community showed differentiations in several function categories. For example, the SA and SB indicative communities showed higher RAs in aerobic chemoheterotrophy, the CSS indicative community showed higher RAs in sulfate respiration, the AD indicative community showed higher RAs in fermentation, and the WB indicative community included higher RAs of predatory/exoparasitic bacteria. Three molecular ecological networks of the communities from the AD, WB and SB datasets were constructed, respectively. The WB network showed the highest proportion of negative correlations (70.4%), possibly attributed to the environmental pressure which aggravated microbial competition. The positively correlated taxa showed lower phylogenetic distances than the negatively correlated taxa on average in each network.

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