scholarly journals Mono-specific algal diets shape microbial networking in the gut of the sea urchin Tripneustes gratilla elatensis

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Matan Masasa ◽  
Ariel Kushmaro ◽  
Esti Kramarsky-Winter ◽  
Muki Shpigel ◽  
Roy Barkan ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Niche Breadth ◽  
Sea Urchins ◽  
Algal Species ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Potential Contribution ◽  
Tripneustes Gratilla ◽  
Algal Diets

Abstract Background Algivorous sea urchins can obtain energy from a diet of a single algal species, which may result in consequent changes in their gut microbe assemblies and association networks. Methods To ascertain whether such changes are led by specific microbes or limited to a specific region in the gut, we compared the microbial assembly in the three major gut regions of the sea urchin Tripneustes gratilla elatensis when fed a mono-specific algal diet of either Ulva fasciata or Gracilaria conferta, or an algal-free diet. DNA extracts from 5 to 7 individuals from each diet treatment were used for Illumina MiSeq based 16S rRNA gene sequencing (V3–V4 region). Niche breadth of each microbe in the assembly was calculated for identification of core, generalist, specialist, or unique microbes. Network analyzers were used to measure the connectivity of the entire assembly and of each of the microbes within it and whether it altered with a given diet or gut region. Lastly, the predicted metabolic functions of key microbes in the gut were analyzed to evaluate their potential contribution to decomposition of dietary algal polysaccharides. Results Sea urchins fed with U. fasciata grew faster and their gut microbiome network was rich in bacterial associations (edges) and networking clusters. Bacteroidetes was the keystone microbe phylum in the gut, with core, generalist, and specialist representatives. A few microbes of this phylum were central hub nodes that maintained community connectivity, while others were driver microbes that led the rewiring of the assembly network based on diet type through changes in their associations and centrality. Niche breadth agreed with microbes' richness in genes for carbohydrate active enzymes and correlated Bacteroidetes specialists to decomposition of specific polysaccharides in the algal diets. Conclusions The dense and well-connected microbial network in the gut of Ulva-fed sea urchins, together with animal's rapid growth, may suggest that this alga was most nutritious among the experimental diets. Our findings expand the knowledge on the gut microbial assembly in T. gratilla elatensis and strengthen the correlation between microbes’ generalism or specialism in terms of occurrence in different niches and their metabolic arsenal which may aid host nutrition.

scholarly journals Interplay between Fungal Infection and Bacterial Associates in the Wax Moth Galleria mellonella under Different Temperature Conditions

2020 ◽  
Vol 6 (3) ◽  
pp. 170
Author(s):  
Vadim Yu Kryukov ◽  
Elena Kosman ◽  
Oksana Tomilova ◽  
Olga Polenogova ◽  
Ulyana Rotskaya ◽  
...  
Keyword(s):  
Fungal Infection ◽  
Bacterial Communities ◽  
Galleria Mellonella ◽  
Fungal Growth ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Cultivable Bacteria ◽  
Stress Related Genes ◽  
Rrna Gene Sequencing

Various insect bacterial associates are involved in pathogeneses caused by entomopathogenic fungi. The outcome of infection (fungal growth or decomposition) may depend on environmental factors such as temperature. The aim of this study was to analyze the bacterial communities and immune response of Galleria mellonella larvae injected with Cordyceps militaris and incubated at 15 °C and 25 °C. We examined changes in the bacterial CFUs, bacterial communities (Illumina MiSeq 16S rRNA gene sequencing) and expression of immune, apoptosis, ROS and stress-related genes (qPCR) in larval tissues in response to fungal infection at the mentioned temperatures. Increased survival of larvae after C. militaris injection was observed at 25 °C, although more frequent episodes of spontaneous bacteriosis were observed at this temperature compared to 15 °C. We revealed an increase in the abundance of enterococci and enterobacteria in the midgut and hemolymph in response to infection at 25 °C, which was not observed at 15 °C. Antifungal peptide genes showed the highest expression at 25 °C, while antibacterial peptides and inhibitor of apoptosis genes were strongly expressed at 15 °C. Cultivable bacteria significantly suppressed the growth of C. militaris. We suggest that fungi such as C. militaris may need low temperatures to avoid competition with host bacterial associates.

scholarly journals High-throughput 16S rRNA gene sequencing of the microbial community associated with palm oil mill effluents of two oil processing systems

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Benedicte Ella Zranseu Aka ◽  
Theodore N’dede Djeni ◽  
Simon Laurent Tiemele Amoikon ◽  
Jan Kannengiesser ◽  
Naaila Ouazzani ◽  
...  
Keyword(s):  
Microbial Community ◽  
Palm Oil ◽  
Microbial Community Composition ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Industrial Plants ◽  
Oil Processing ◽  
Microbial Contaminants ◽  
Palm Oil Mill

AbstractPalm Oil Mill Effluents (POME) are complex fermentative substrates which habour diverse native microbial contaminants. However, knowledge on the microbiota community shift caused by the anthropogenic effects of POME in the environment is up to date still to be extensively documented. In this study, the bacterial and archaeal communities of POME from two palm oil processing systems (artisanal and industrial) were investigated by Illumina MiSeq Platform. Despite the common characteristics of these wastewaters, we found that their microbial communities were significantly different with regard to their diversity and relative abundance of their different Amplicon Sequence Variants (ASV). Indeed, POME from industrial plants harboured as dominant phyla Firmicutes (46.24%), Bacteroidetes (34.19%), Proteobacteria (15.11%), with the particular presence of Spirochaetes, verrucomicrobia and Synergistetes, while those from artisanal production were colonized by Firmicutes (92.06%), Proteobacteria (4.21%) and Actinobacteria (2.09%). Furthermore, 43 AVSs of archaea were detected only in POME from industrial plants and assigned to Crenarchaeota, Diapherotrites, Euryarchaeota and Nanoarchaeaeota phyla, populated mainly by many methane-forming archaea. Definitively, the microbial community composition of POME from both type of processing was markedly different, showing that the history of these ecosystems and various processing conditions have a great impact on each microbial community structure and diversity. By improving knowledge about this microbiome, the results also provide insight into the potential microbial contaminants of soils and rivers receiving these wastewaters.

scholarly journals Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

2013 ◽  
Vol 80 (2) ◽  
pp. 757-765 ◽  
Author(s):  
Amber M. Koskey ◽  
Jenny C. Fisher ◽  
Mary F. Traudt ◽  
Ryan J. Newton ◽  
Sandra L. McLellan
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Fecal Indicator ◽  
Fecal Samples ◽  
Content Type

ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such asEscherichia coliand enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.EnterococcaceaeandEnterobacteriaceaewere the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealedCatellicoccus marimammaliumas the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcusindoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified asEnterococcusspp., 1.2% were identified asStreptococcusspp., and none were identified asC. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions ofC. marimammalium16S rRNA gene sequences (>50-fold) relative to typical mEI culturableEnterococcusspp.C. marimammaliumtherefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment.

scholarly journals Biophotonics for Biofuel Upgradation

2017 ◽  
Vol 25 (4) ◽  
pp. 262-266
Author(s):  
Gopinath Rana ◽  
Tanusri Mandal
Keyword(s):  
Carbon Dioxide ◽  
Flame Temperature ◽  
Experimental Studies ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Fuel Gas ◽  
Photo Bioreactor ◽  
Rrna Gene Sequencing ◽  
Downstream Analysis

AbstractExperimental studies have been made to find out Cyanobacterias’ biophotonical response in gaseous-fuelation and carbon dioxide fixation during photo-anaerobic digestion. A new horizontal type photo-bioreactor has been designed by using environment hazard plastic bottles and it works ideally for anoxygenic cyanobacterial growth. Through ‘V3-metagenomics’ of 16S rRNA gene sequencing by paired-end Illumina MiSeq and downstream analysis by QIIME program, we have identified anaerobic cyanobacteria, represent the orders YS2 and Streptophyta. OTUs have been identified by aligning against Greengenes and Silva databases, separately. The flame temperature of the fuel gas is 860°C and the percent-content of carbon dioxide (CO2) is 17.6%.

scholarly journals Arenicella chitinivorans sp. nov., a gammaproteobacterium isolated from the sea urchin Strongylocentrotus intermedius

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4124-4129 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Ilse Cleenwerck ◽  
Natalia V. Zhukova ◽  
Seung Bum Kim ◽  
Paul de Vos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchin ◽  
Type Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A strictly aerobic, Gram-stain-negative, rod-shaped, non-motile and yellow-pigmented bacterial strain, designated KMM 6208T, was isolated from a sea urchin. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that this novel isolate was affiliated to the class Gammaproteobacteria and formed a robust cluster with Arenicella xantha KMM 3895T with 98.2 % 16S rRNA gene sequence similarity. Strain KMM 6208T grew in the presence of 0.5–5 % NaCl and at a temperature range of 4–38 °C. The isolate was oxidase-positive and hydrolysed aesculin, casein, chitin, gelatin, starch and Tweens 40 and 80. The prevalent fatty acids of strain KMM 6208T were C16 : 1ω7c, iso-C16 : 0, iso-C18 : 0, C18 : 1ω7c and C16 : 0. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified aminophospholipid, and the major isoprenoid quinone was Q-8. The DNA G+C content of strain KMM 6208T was 46.3 mol%. The DNA–DNA relatedness value of strain KMM 6208T with Arenicella xantha KMM 3895T was 5 %. Molecular data in a combination with phenotypic findings strongly suggest inclusion of this novel strain in the genus Arenicella as a representative of a novel species for which the name Arenicella chitinivorans sp. nov. is proposed. The type strain is KMM 6208T ( = KCTC 12711T = LMG 26983T).

scholarly journals Hard time to be parents? Sea urchin fishery shifts potential reproductive contribution of population onto the shoulders of the youngest

2016 ◽  
Author(s):  
Barbara Loi ◽  
Ivan Guala ◽  
Rodrigo Pires da Silva ◽  
Gianni Brundu ◽  
Maura Baroli ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Sea Urchins ◽  
Gonadosomatic Index ◽  
Reproductive Potential ◽  
Size Class ◽  
High Density ◽  
Similar Amount ◽  
Potential Contribution ◽  
Total Density ◽  
Commercial Size

Background. In Sardinia, as in other regions of the Mediterranean Sea, sustainable fisheries of the sea urchin Paracentrotus lividus have become a necessity. At harvesting sites, the systematic removal of large individuals (diameter ≥ 50 mm) seriously compromises the biological and ecological functions of sea urchin populations. Specifically, in this study, we compared the reproductive potential of the populations from two Mediterranean coastal sites which have different levels of protection. The sites were Su Pallosu, where fishing pressure is high (take zone) and at Tavolara-Punta Coda Cavallo Marine Protected Area (no-take zone) where the pressure is negligible. Methods. Reproductive potential was estimated by calculating Gonadosomatic Index (GSI) from June 2013 to May 2014 both for individuals of commercial size (diameter without spines, TD ≥ 50 mm) and the undersized ones with gonads (30 ≤ TD < 40 mm and 40 ≤ TD < 50 mm). Gamete Output was calculated for the commercial-size class and the undersized individuals with fertile gonads (40 ≤ TD < 50 mm) in relation to their natural density (Gamete Output per m2). Results. The reproductive potential of populations was slightly different at the beginning of the sampling period but it progressed at different rates with an early spring spawning event in the take zone and two gamete depositions in early and late spring in the no-take zone. For each fertile size class, GSI values changed significantly during the year of our study and between the two levels of protection. Although the multiple spawning events determined a two-fold higher total Gamete Output of population (popTGO) in the no-take zone, the population Mean Gamete Output (popMGO) was similar in the two zones. In the take zone, the commercial-sized individuals represented approximatively 5% of the population, with almost all the individuals smaller than 60 mm producing an amount of gametes nearly three times lower than the undersized ones. Conversely, the high density of the undersized individuals released a similar amount of gametes to the commercial-size class in the no-take zone. Discussion. Overall, the lack of the commercial-size class in the take zone does not seem to be very alarming for the self-supporting capacity of the population, and the reproductive potential contribution seems to depend more on the total density of fertile sea urchins than on their size. However, since population survival in the take zone is supported by the high density of undersized sea urchins between 30 and 50 mm, management measures should be addressed to maintain this size and to shed light on the source of the larval supply.

scholarly journals Chryseobacterium echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla)

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3985-3990 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
Cheng-Zhe Wen ◽  
You-Cheng Liu ◽  
Fo-Ting Shen ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchins ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Tripneustes Gratilla

A Gram-stain-negative, aerobic, non-motile, rod-shaped, flexirubin-producing bacterium, designated strain CC-CZW010T, was isolated from the edible sea urchin Tripneustes gratilla in Penghu Island, Taiwan. The isolate grew optimally at pH 7.0 and 30 °C in the presence of 2 % (w/v) NaCl. The most closely related strains in terms of 16S rRNA gene sequence similarity were Chryseobacterium taihuense NBRC 108747T (97.6 %) and Chryseobacterium aquaticum KCTC 12483T (96.7 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed a distinct taxonomic position attained by strain CC-CZW010T with respect to other species of the genus Chryseobacterium. Strain CC-CZW010T possessed iso-C15 : 0, anteiso-C15 : 0, iso-C17 :  0 3-OH, summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) and summed feature 9 (comprising C16 :  0 10-methyl/iso-C17 : 1ω9c) as predominant fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified lipids and five aminolipids. The polyamine pattern contained the major compound sym-homospermidine. Menaquinone 6 (MK-6) was the predominant respiratory quinone, and the G+C content of the genomic DNA was 36.4 mol%. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-CZW010T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium echinoideorum sp. nov. is proposed. The type strain is CC-CZW010T ( = BCRC 80786T = JCM 30470T).

Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice

2021 ◽  
pp. annrheumdis-2020-219009
Author(s):  
Rabia Moentadj ◽  
Yiwen Wang ◽  
Kate Bowerman ◽  
Linda Rehaume ◽  
Hendrik Nel ◽  
...  
Keyword(s):  
Operational Taxonomic Unit ◽  
16S Rrna Gene Sequencing ◽  
Chronic Arthritis ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Potential Contribution ◽  
Barrier Dysfunction ◽  
Microbial Dysbiosis ◽  
Periodontal Inflammation

ObjectivesAnalysis of oral dysbiosis in individuals sharing genetic and environmental risk factors with rheumatoid arthritis (RA) patients may illuminate how microbiota contribute to disease susceptibility. We studied the oral microbiota in a prospective cohort of patients with RA, first-degree relatives (FDR) and healthy controls (HC), then genomically and functionally characterised streptococcal species from each group to understand their potential contribution to RA development.MethodsAfter DNA extraction from tongue swabs, targeted 16S rRNA gene sequencing and statistical analysis, we defined a microbial dysbiosis score based on an operational taxonomic unit signature of disease. After selective culture from swabs, we identified streptococci by sequencing. We examined the ability of streptococcal cell walls (SCW) from isolates to induce cytokines from splenocytes and arthritis in ZAP-70-mutant SKG mice.ResultsRA and FDR were more likely to have periodontitis symptoms. An oral microbial dysbiosis score discriminated RA and HC subjects and predicted similarity of FDR to RA. Streptococcaceae were major contributors to the score. We identified 10 out of 15 streptococcal isolates as S. parasalivarius sp. nov., a distinct sister species to S. salivarius. Tumour necrosis factor and interleukin 6 production in vitro differed in response to individual S. parasalivarius isolates, suggesting strain specific effects on innate immunity. Cytokine secretion was associated with the presence of proteins potentially involved in S. parasalivarius SCW synthesis. Systemic administration of SCW from RA and HC-associated S. parasalivarius strains induced similar chronic arthritis.ConclusionsDysbiosis-associated periodontal inflammation and barrier dysfunction may permit arthritogenic insoluble pro-inflammatory pathogen-associated molecules, like SCW, to reach synovial tissue.

scholarly journals Microbial Diversity of the Red Sea Urchin Loxechinus albus during Controlled Farming in Puerto Montt, Chile, Using 16S rRNA Gene Amplicon Sequencing

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Daniel A. Medina ◽  
Rudy Suárez ◽  
Marcos Godoy
Keyword(s):  
16S Rrna ◽  
Sea Urchin ◽  
Cold Water ◽  
Sea Urchins ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Rrna Sequencing ◽  
Red Sea Urchin ◽  
Loxechinus Albus

Loxechinus albus is a shallow-water sea urchin, and its distribution is related to the cold water of the Southern Hemisphere. Recently, bacterial communities, also called microbiota, in sea urchins have started being explored. In this report, we have characterized the surface, testa, and gonad microbiota using 16S rRNA sequencing.

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