scholarly journals Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4970 ◽  
Author(s):  
Ton That Huu Dat ◽  
Georg Steinert ◽  
Nguyen Thi Kim Cuc ◽  
Hauke Smidt ◽  
Detmer Sipkema
Keyword(s):  
Coastal Region ◽  
Illumina Miseq ◽  
Sponge Species ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Prokaryotic Diversity ◽  
Class Level ◽  
Wide Range ◽  
Host Identity ◽  
Species Specific

Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylumProteobacteriawas present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast,Chloroflexiwas the most abundant phylum inHalichondriasp., whereasSpirastrellasp. andDactylospongiasp. were dominated byActinobacteria. Several bacterial phyla such asAcidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, andNitrospiraewere found in two-thirds of the sponge species. Moreover, the phylumThaumarchaeota(Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.

scholarly journals Microbiomes of the Arctic carnivorous sponges Chondrocladia grandis and Cladorhiza oxeata suggest a specific, but differential involvement of bacterial associates

2018 ◽  
Vol 4 (2) ◽  
pp. 186-204 ◽  
Author(s):  
Joost T.P. Verhoeven ◽  
Suzanne C. Dufour
Keyword(s):  
Bacterial Communities ◽  
Gulf Of Maine ◽  
Bacterial Community Composition ◽  
Isotope Analysis ◽  
Taxonomic Diversity ◽  
The Arctic ◽  
Sponge Species ◽  
Rrna Gene ◽  
Wide Range ◽  
Species Specific

While sponges are generally known to host a wide range of microbial associates, the composition and specificity of the microbial communities in carnivorous sponges are poorly understood. We used 16S rRNA gene data to examine and compare the bacterial communities associated with distinct anatomical regions of two carnivorous sponge species, Chondrocladia grandis and Cladorhiza oxeata, sampled from Baffin Bay and the Gulf of Maine (C. grandis only). The two sponge species hosted distinct bacterial communities, with taxonomic diversity being greater in C. grandis. Some bacterial taxa (including particular oligotypes) were consistently recovered in multiple host individuals from geographically distant sites, suggesting specificity. Within C. grandis, certain bacterial taxa were enriched in particular anatomical regions, suggesting functional roles in carnivorous sponge metabolism or other biological processes. Stable isotope analysis provided no evidence for methanotrophy in the sponges examined, but Gulf of Maine C. grandis might incorporate 13C-depleted carbon via the bacteria-mediated heterotrophic degradation of other hydrocarbons. Overall, our results demonstrate that the carnivorous sponge microbiome appears host species specific and stable, even over large geographical areas. The observed differences in bacterial community composition and diversity between C. grandis and C. oxeata may reflect differences in trophic adaptability, specialization, and overall reliance on associated bacteria.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Lieven Waeyenberge ◽  
Nicole Viaene ◽  
Maurice Moens
Keyword(s):  
Internal Control ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Duplex Pcr ◽  
Specific Primers ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Wide Range ◽  
Pcr Products ◽  
Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

scholarly journals Influence of Agaricus Bisporus Establishment and Fungicidal Treatments on Casing Soil Metataxonomy During Mushroom Cultivation

2021 ◽  
Author(s):  
Maria Luisa Tello ◽  
Rebeca Lavega ◽  
Margarita Pérez ◽  
Antonio J. Pérez ◽  
Michael Thon ◽  
...  
Keyword(s):  
Agaricus Bisporus ◽  
Illumina Miseq ◽  
Biological Efficiency ◽  
Its2 Region ◽  
Rrna Gene ◽  
Mushroom Cultivation ◽  
Microbial Composition ◽  
Mycelium Growth ◽  
Bacterial Phyla ◽  
The Impact

Abstract The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. Mushrooms are a source of resources still to be revealed, which have applications not only in food, but in many other sectors such as health, industry and biotechnology. Mushroom cultivation consists of the development of selective substrates through composting where the mushroom grows via solid fermentation process. In case of Agaricus bisporus, the compost fully colonized by mycelium hardly produces mushrooms and it is necessary to apply a casing layer with certain physical, chemical and biological characteristics to shift from the vegetative mycelium to the reproductive one, where the native microbiota plays crucial roles. Currently, the industry faces a challenge to substitute the actual peat based casing materials due to the limited natural resources and the impact on the peatlands where peat is extracted.In this work we have employed high-throughput techniques by next generation sequencing to screen the microbial structure of casing soil employed in mushroom cultivation while sequencing V3-V4 of the 16S rRNA gene for bacteria and the ITS2 region of rRNA for fungi in an Illumina MiSeq. In addition, the microbiome dynamics and evolution (bacterial and fungal communities) in peat based casing along the process of incubation of Agaricus bisporus have been studied, while comparing the effect of fungicidal treatment (Chlorothalonil and Metrafenone). Statistically significant changes in populations of bacteria and fungi were observed. Microbial composition differed significantly based on incubation day, changing radically from the original communities to a specific microbial composition adapted to enhance the A. bisporus mycelium growth. Chlorothalonil treatment seems to delay casing colonization by A. bisporus. Proteobacteria and Bacteroidota appeared as the most dominant bacterial phyla. We observed a great change in the structure of the bacteria populations between day 0 and the following days. Fungi populations changed more gradually, A. bisporus displacing the rest of the species as the cultivation cycle progresses. A better understanding of the microbial communities in the casing will hopefully allow us to increase the biological efficiency during production as well as possibly help us to have a clearer view of the microbial community-pathogen relationships as they are directly related to disease development.

scholarly journals Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rafael J. Vivero ◽  
Marcela Villegas-Plazas ◽  
Gloria E. Cadavid-Restrepo ◽  
Claudia Ximena Moreno Herrera ◽  
Sandra I. Uribe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Sand Fly ◽  
Human Populations ◽  
Rrna Gene ◽  
Remarkable Feature ◽  
Core Microbiome ◽  
Bacterial Phyla ◽  
Wide Range

AbstractPhlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.

Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
Hui Yao ◽  
Xiang Sun ◽  
Chao He ◽  
Xing-Chun Li ◽  
Liang-Dong Guo
Keyword(s):  
Community Structure ◽  
Endophytic Bacteria ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Network Structures ◽  
Community Structures ◽  
Mangrove Species ◽  
Host Identity ◽  
Biodiversity Maintenance ◽  
Endophytic Bacterial Community

ABSTRACT Interactions between plants and microbes are involved in biodiversity maintenance, community stability and ecosystem functioning. However, differences in the community and network structures between phyllosphere epiphytic and endophytic bacteria have rarely been investigated. Here, we examined phyllosphere epiphytic and endophytic bacterial communities of six mangrove species using Illumina MiSeq sequencing of the 16S rRNA gene. The results revealed that the community structure of epiphytic and endophytic bacteria was different. Plant identity significantly affected the diversity and community structure of both epiphytic and endophytic bacteria, with a greater effect on the community structure of the former than the latter. Network analysis showed that both plant–epiphytic and plant–endophytic bacterial network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the epiphytic bacterial network was more highly specialized and modular but less connected and more strongly anti-nested than the endophytic bacterial network. This study reveals that the phyllosphere epiphytic and endophytic bacterial community structures differ and plant identity has a greater effect on the epiphytic than on the endophytic bacteria, which may provide a comprehensive insight into the role of plant identity in driving the phyllosphere epiphytic and endophytic microbial community structures in mangrove ecosystems.

scholarly journals The Liquid Diet Composition Affects the Fecal Bacterial Community in Pre-weaning Dairy Calves

2021 ◽  
Vol 2 ◽  
Author(s):  
Gercino Ferreira Virgínio Júnior ◽  
Marina Gavanski Coelho ◽  
Ariany Faria de Toledo ◽  
Horácio Montenegro ◽  
Luiz Lehmann Coutinho ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Diet Composition ◽  
Illumina Miseq ◽  
Liquid Diet ◽  
Free Access ◽  
Rrna Gene ◽  
Fecal Samples ◽  
Bacterial Phyla ◽  
Whole Milk ◽  
Fecal Bacterial Community

Feeding a liquid diet to the newborn calf has considerable implications for developing the intestinal microbiota, as its composition can shift the population to a highly adapted microbiota. The present work evaluated 15 Holstein calves individually housed and fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9% CP; 16.2% fat; diluted to 14% solids; n = 5) and III – acidified whole milk to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at week 8 of life. Calves also had free access to water and starter concentrate. After weaning, all calves were grouped on pasture, fed with starter concentrate, and hay ad libitum. The fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8, and 10 of life. The bacterial community was assessed the through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. Diversity indices were not affected by the liquid diets, but by age (P < 0.001) with weeks 1 and 2 presenting lower diversity, evenness, and richness values. The bacterial community structure was affected by diet, age, and the interaction of these factors (P < 0.01). Twenty-eight bacterial phyla were identified in the fecal samples, and the most predominant phyla were Firmicutes (42.35%), Bacteroidota (39.37%), and Proteobacteria (9.36%). The most prevalent genera were Bacteroides (10.71%), Lactobacillus (8.11%), Alloprevotella (6.20%). Over the weeks, different genera were predominant, with some showing significant differences among treatments. The different liquid diets altered the fecal bacterial community during the pre-weaning period. However, differences in the initial colonization due to different liquid diets are alleviated after weaning, when animals share a common environment and solid diet composition.

scholarly journals A Metagenomic Analysis of the Equine Gut Microbiome with and Without Probiotic Supplementation (P09-006-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Olivia Konen ◽  
Kristin Peters ◽  
Petra Tsuji
Keyword(s):  
Relative Abundance ◽  
Illumina Miseq ◽  
Experimental Manipulation ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Probiotic Supplementation ◽  
Fecal Matter ◽  
Microbiome Composition ◽  
Bacterial Phyla ◽  
And Mathematics

Abstract Objectives The goal of this study is to compare the microbiome of domesticated horses with and without probiotic supplementation. Methods Our University's Institutional Animal Care and Use Committee has granted an exemption, as the horses were not housed on campus and there was no experimental manipulation to the horses’ feeding implemented. Fecal matter from six privately owned horses maintained on their standard grazing diet were collected. Three of the six horses received a probiotic supplement, SmartDigest, for several years prior to beginning the project. Supplementation ceased for one month, and samples were again obtained. The other three horses never received probiotics. Bacterial DNA was isolated from all fecal samples, the 16S rRNA gene amplified, tagged with index primers, and subsequently sequenced using the Illumina MiSeq. Results Dominant groups from non-supplemented horses residing on the same property included the phyla bacteriodetes, firmicutes, proteobacteria, and verrucomicrobia. Interestingly, Sphingobacterium bambusae was identified in all three horses, even though this species has previously been isolated from the soil of bamboo plantations. Currently, samples from horses with probiotics are being analyzed. We are also employing qPCR analysis to validate the NextGen data, and to further investigate relative abundance of specific bacterial groups relevant to equine intestinal health. Conclusions Preliminary NextGen sequence analysis of the relative abundance of bacterial phyla suggests that, as expected, the horses residing on the same property and thus receiving the same diet possess a similar intestinal microbiome composition. Similarities between horses persist down to the genus level, and are now being compared to samples from horses on a probiotic-supplemented diet. Funding Sources Financial support was provided by Towson University's Fisher College of Science and Mathematics, and Jess and Mildred Fisher Endowed Chair funds to P. Tsuji.

Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum ‘ Chloroflexi ’ isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov.

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2992-3002 ◽  
Author(s):  
Satoshi Kawaichi ◽  
Norihiro Ito ◽  
Ryoma Kamikawa ◽  
Tatsuya Sugawara ◽  
Takashi Yoshida ◽  
...  
Keyword(s):  
New Genus ◽  
Ferric Iron ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
New Class ◽  
Link Type ◽  
Class Level ◽  
Wide Range

A novel thermophilic, chemoheterotrophic, Gram-negative-staining, multicellular filamentous bacterium, designated strain 110ST, was isolated from an iron-rich coastal hydrothermal field in Japan. The isolate is facultatively aerobic and chemoheterotrophic. Phylogenetic analysis using 16S rRNA gene sequences nested strain 110ST in a novel class-level clone cluster of the phylum ‘ Chloroflexi ’. The isolate grows by dissimilatory iron- and nitrate-reduction under anaerobic conditions, which is the first report of these abilities in the phylum ‘ Chloroflexi ’. The organism is capable of growth with oxygen, ferric iron and nitrate as a possible electron acceptor, has a wide range of growth temperatures, and tolerates higher NaCl concentrations for growth compared to the other isolates in the phylum. Using phenotypic and phylogenetic data, strain 110ST ( = JCM 17282T = NBRC 107679T = DSM 23922T = KCTC 23289T = ATCC BAA-2145T) is proposed as the type strain of a novel species in a new genus, Ardenticatena maritima gen. nov., sp. nov. In addition, as strain 110ST apparently constitutes a new class of the phylum ‘ Chloroflexi ’ with other related uncultivated clone sequences, we propose Ardenticatenia classis nov. and the subordinate taxa Ardenticatenales ord. nov. and Ardenticatenaceae fam. nov.

scholarly journals PSVI-22 Fecal microbiome of dairy calves fed with different liquid diets

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 431-431
Author(s):  
Gercino F Virgínio Júnior ◽  
Marina Coelho ◽  
Marcos Silva ◽  
Horácio Montenegro ◽  
Luiz Coutinho ◽  
...  
Keyword(s):  
Animal Health ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Liquid Diet ◽  
Intestinal Microbiome ◽  
Milk Replacer ◽  
Rrna Gene ◽  
Fecal Microbiome ◽  
Bacterial Phyla ◽  
Whole Milk

Abstract Feeding a liquid diet to the newborn calf has considerable implications for the development of the intestinal microbiota, as its composition can shift population to a highly adapted microbiota. Milk acidification may positively affect microorganisms that are beneficial to the intestine health. The present study evaluated 15 Holstein calves housed in tropical shelters, fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9 % CP; 18.5 % fat; diluted to 14% solids; n = 5) and III - whole milk acidified to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at the 8th week of age. After weaning, all calves were group housed and fed with starter concentrate and coast-cross hay ad libitum. To evaluate the microbioma, fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. The diversity indices and evenness were higher for whole milk when compared to milk replacer (P < 0,05), with no difference for acidified whole milk. Animal age affected all indices. Time 0 had higher richness and diversity (P < 0,001), while weeks 1 and 2 had the lowest (P < 0,001). Thirty-eight bacterial phyla were identified, and the most abundant in were Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria and Firmicutes C. It is possible to modify the microbiome by changing the liquid diet. However, differences according to calf age may show the best time for possible interventions in the diet to manipulate the intestinal microbiome to improve animal health and performance.

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