community profile
Recently Published Documents


TOTAL DOCUMENTS

101
(FIVE YEARS 33)

H-INDEX

12
(FIVE YEARS 3)

Author(s):  
Meike Anna Christine Latz ◽  
Vesna Grujcic ◽  
Sonia Brugel ◽  
Jenny Lycken ◽  
Bengt Karlson ◽  
...  

High-throughput sequencing for analysis of environmental microbial diversity has evolved vastly over the last decade. Currently the go-to method for microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics datasets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.


2021 ◽  
Vol 12 ◽  
Author(s):  
Merve Atasoy ◽  
Zeynep Cetecioglu

Production of targeted volatile fatty acid (VFA) composition by fermentation is a promising approach for upstream and post-stream VFA applications. In the current study, the bioaugmented mixed microbial culture by Clostridium aceticum was used to produce an acetic acid dominant VFA mixture. For this purpose, anaerobic sequencing batch reactors (bioaugmented and control) were operated under pH 10 and fed by cheese processing wastewater. The efficiency and stability of the bioaugmentation strategy were monitored using the production and composition of VFA, the quantity of C. aceticum (by qPCR), and bacterial community profile (16S rRNA Illumina Sequencing). The bioaugmented mixed culture significantly increased acetic acid concentration in the VFA mixture (from 1170 ± 18 to 122 ± 9 mgCOD/L) compared to the control reactor. Furthermore, the total VFA production (from 1254 ± 11 to 5493 ± 36 mgCOD/L) was also enhanced. Nevertheless, the bioaugmentation could not shift the propionic acid dominancy in the VFA mixture. The most significant effect of bioaugmentation on the bacterial community profile was seen in the relative abundance of the Thermoanaerobacterales Family III. Incertae sedis, its relative abundance increased simultaneously with the gene copy number of C. aceticum during bioaugmentation. These results suggest that there might be a syntropy between species of Thermoanaerobacterales Family III. Incertae sedis and C. aceticum. The cycle analysis showed that 6 h (instead of 24 h) was adequate retention time to achieve the same acetic acid and total VFA production efficiency. Biobased acetic acid production is widely applicable and economically competitive with petroleum-based production, and this study has the potential to enable a new approach as produced acetic acid dominant VFA can replace external carbon sources for different processes (such as denitrification) in WWTPs. In this way, the higher treatment efficiency for WWTPs can be obtained by recovered substrate from the waste streams that promote a circular economy approach.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raiza Hasrat ◽  
Jolanda Kool ◽  
Wouter A. A. de Steenhuijsen Piters ◽  
Mei Ling J. N. Chu ◽  
Sjoerd Kuiling ◽  
...  

AbstractThe low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.


2021 ◽  
Vol 60 (2) ◽  
pp. 59-74
Author(s):  
Asst. Inst. Tiba Abdulkareem Al-Obaidi

This study investigates the language situation of the Armenian language among the Armenians of Baghdad. The researcher examines the domains of language where the Armenians use their ethnic language and the factors that support them use their ethnic language side by side with Arabic language. The researcher uses a pilot questionnaire that helped her to create a community profile which gives information about the community. She uses a sociolinguistic questionnaire, which is formed by the information taken from pilot questionnaire, to answer the main questions of the study. She distributed the questionnaire to 50 participants from different demographic background from Armenian community. The study concludes that the Armenians of Baghdad still preserve their ethnic language and use it restrictedly at home, church and in social religious events. The study also finds that the home, the family and the church are the major factors that maintain the Armenian language among the community in Baghdad. It also shows other factors that maintain the Armenian language such as schools, institutions, and the historic events that live in the memory of the community that contribute to the language maintenance.


2021 ◽  
Vol 56 (2) ◽  
pp. 256-271
Author(s):  
Desmond Onyeka Agwunobi ◽  
Joshua Kamani ◽  
Hongyuan Zheng ◽  
Lida Guo ◽  
Zhijun Yu ◽  
...  

Abstract Rhipicephalus sanguineus (Latreille) is the most widely distributed tick species globally and plays a major role in tick-borne pathogen transmission among canine populations. The microbial community of this tick has not been characterized previously in Nigeria. Thus, in this study, the bacterial diversity in R. sanguineus collected from two states in Nigeria was explored using 16S rRNA high-throughput sequencing (IonS5TM XL sequencing platform). Three hundred genera (although 18 groups belong to unidentified genera) of bacteria belonging to 22 phyla were detected after pooling and sequencing, indicating a diverse bacterial community profile. At the phylum level, Actinobacteria (47.39%) was the most abundant phylum in the Benue state samples, followed by Proteobacteria (43.87%) and Firmicutes (8.21%), whereas Fusobacteria (38.14%) was the most abundant phylum in Plateau state samples, followed by Bacteroidetes (17.57%) and Firmicutes (17.54%). Proteobacteria accounts for 17% of samples from Plateau state. In general, Cetobacterium (35.86%) was the most abundant genus, followed by an unidentified genus under Corynebacteriaceae (29.94%) and Stenotrophomonas (19.52%). Coxiella spp., one common endosymbiont found in various tick species, was present in R. sanguineus. This study provides a baseline of knowledge of the bacterial microbiome of R. sanguineus in Nigeria. Nonpathogenic bacteria species were prevalent, and not much is known about their role. Thus, their composition, functional, and ecologic implications merit further investigation because this will aid in the subsequent management of ticks and tick-borne diseases.


2021 ◽  
Vol 4 ◽  
Author(s):  
E. Gozde Ozbayram ◽  
Latife Koker ◽  
Reyhan Akçaalan ◽  
Fatih Aydın ◽  
Meriç Albay

Lake Iznik is one of the largest lake of Turkey covering 308 km2 surface area with 65 m max. depth. The lake has alkaline characteristics (Akcaalan et al. 2014). It is a mesotrophic lake that becomes stratified between June-September and well mixed between October-April. Although there are almost 200 lakes in Turkey, there is very little published research focused on the bacterial diversity structures (Ozbayram et al. 2020.) The specific objective of this study was to evaluate the bacterial community profile in the surface water and sediment of the alkaline lake during the winter turnover. For this purpose, the samples were collected from 6 stations (5 on the shore and 1 in the middle of the lake) in February 2020 when the lake was completely mixed. In addition to the surface water and sediment samples, a sample was also collected from the depth of 40 m from the station located in the mid-lake. The water samples were filtered from a 0.22 µm filter and the sediment samples were taken into sterile plastic containers. The total DNAs were extracted using the NucleoSpin® Soil Kit (Macherey-Nagel, Germany) following the manufacturer’s instructions. Bacterial community profiles of the samples were analyzed by 16S rRNA gene-targeted sequencing using Illumina® MiSeq™. Physicochemical parameters were measured as explained by Ozbayram et al. 2020. The pH was between 8.29-8.67 and the Electrical Conductivity (EC) was in the range of 734-996 µS/cm (Suppl. material 1 -Table S1). Whereas the Dissolved Oxygen (DO) levels were measured as 10.12-11.65 mg/L in the surface waters, it was 9.72 mg/L in the 40 m. Among all samples, the highest value of the Shannon and Pielou's evenness indices were calculated for the surface water sample collected from station 2 indicated a more evenly distributed and diverse bacterial community (Suppl. material 1-Table S2). Bacterial diversity patterns of the samples were presented at the phylum level in Figure 1. In compliance with the literature on freshwaters (Zhang et al. 2014), the community was dominated by Proteobacteria species, and higher abundances were determined in the sediment samples (ranged 40.4-50.0 %). Especially, Gammaproteobacteria, Deltaproteobacteria were the major classes of this phylum in the sediment. On the other hand, the composition of bacterial communities in water samples showed a difference in which Actinobacteria and Bacteroidetes (in particular, the order: Flavobacteriales) were also predominated the communities. However, the community profile slightly differed with depth (station 6). At the genus level, most of the reads were not assigned any genera. Ilumatobacter, Fluviicola, and Flavobacterium were represented 3.4-7.1% of the bacterial community of water samples. Fig. 1 Overall, due to the complete mixing conditions in the lake, there was a homogenization of the bacterial communities and the diversity patterns were quite similar in the water samples. In further studies, samples will be collected during the stratification and the community structures will be compared.


Sign in / Sign up

Export Citation Format

Share Document