scholarly journals Microbiota composition and evenness predict survival rate of oysters confronted to Pacific Oyster Mortality Syndrome

2018 ◽  
Author(s):  
Camille Clerissi ◽  
Julien de Lorgeril ◽  
Bruno Petton ◽  
Aude Lucasson ◽  
Jean-Michel Escoubas ◽  
...  
Keyword(s):  
Survival Rate ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Pacific Oyster ◽  
Economic Losses ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Disease Dynamics ◽  
Oyster Mortality ◽  
Resistant Family

AbstractPacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and caused important economic losses. Disease dynamics was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 µVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to oyster protection to POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favour of POMS. After five days of transplantation, oysters from each family were either sampled for individual microbiota analyses using 16S rRNA gene-metabarcoding or transferred into facilities to record their survival using controlled condition. As expected, all oysters from susceptible families died, and all oysters from the resistant family survived. Quantification of OsHV-1 and bacteria showed that five days of transplantation was long enough to contaminate oysters by POMS, but not for entering the pathogenesis process. Thus, it was possible to compare microbiota characteristics between resistant and susceptible oyster families at the early steps of infection. Strikingly, we found that microbiota evenness and abundances of Cyanobacteria (Subsection III, family I), Mycoplasmataceae, Rhodobacteraceae, and Rhodospirillaceae were significantly different between resistant and susceptible oyster families. We concluded that these microbiota characteristics might predict oyster mortalities.

Streptomyces rhizophilus Causes Potato Common Scab Disease

Plant Disease ◽  
2021 ◽  
Author(s):  
Qi Wei ◽  
Jie Li ◽  
Shuai Yang ◽  
Wenzhong Wang ◽  
Fanxiang Min ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Common Scab ◽  
Bacterial Species ◽  
Economic Losses ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Heilongjiang Province ◽  
Epidemic Disease ◽  
Genus Streptomyces

Common scab (CS) caused by Streptomyces spp. is a significant soilborne potato disease that results in tremendous economic losses globally. Identification of CS-associated species of the genus Streptomyces can enhance understanding of the genetic variation of these bacterial species and is necessary for the control of this epidemic disease. The present study isolated Streptomyces strain 6-2-1(1) from scabby potatoes in Keshan County, Heilongjiang Province, China. PCR analysis confirmed that the strain harbored the characteristic Streptomyces pathogenicity island (PAI) genes (txtA, txtAB, nec1, and tomA). Pathogenicity assays proved that the strain caused typical scab lesions on potato tuber surfaces and necrosis on radish seedlings and potato slices. Subsequently, the strain was systemically characterized at morphological, physiological, biochemical and phylogenetic levels. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6-2-1(1) shared 99.86% sequence similarity with Streptomyces rhizophilus JR-41T, isolated initially from bamboo in rhizospheric soil in Korea. PCR amplification followed by Sanger sequencing of the 16S rRNA gene of 164 scabby potato samples collected in Heilongjiang Province from 2019 to 2020 demonstrated that approximately 2% of the tested samples were infected with S. rhizophilus. Taken together, these results demonstrate that S. rhizophilus is capable of causing potato CS disease and may pose a potential challenge to potato production in Heilongjiang Province of China.

scholarly journals Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome

2020 ◽  
Vol 11 ◽  
Author(s):  
Camille Clerissi ◽  
Julien de Lorgeril ◽  
Bruno Petton ◽  
Aude Lucasson ◽  
Jean-Michel Escoubas ◽  
...  
Keyword(s):  
Survival Rate ◽  
Pacific Oyster ◽  
Microbiota Composition ◽  
Oyster Mortality

scholarly journals Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

2010 ◽  
Vol 38 (22) ◽  
pp. e200-e200 ◽  
Author(s):  
Marcus J. Claesson ◽  
Qiong Wang ◽  
Orla O'Sullivan ◽  
Rachel Greene-Diniz ◽  
James R. Cole ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals Refinement of 16S rRNA gene analysis for low biomass biospecimens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Remy Villette ◽  
Gaelle Autaa ◽  
Sophie Hind ◽  
Johanna B. Holm ◽  
Alicia Moreno-Sabater ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Extraction ◽  
High Throughput ◽  
Nested Pcr ◽  
Genomic Dna ◽  
Gene Analysis ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
16S Rrna Gene Analysis

AbstractHigh-throughput phylogenetic 16S rRNA gene analysis has permitted to thoroughly delve into microbial community complexity and to understand host-microbiota interactions in health and disease. The analysis comprises sample collection and storage, genomic DNA extraction, 16S rRNA gene amplification, high-throughput amplicon sequencing and bioinformatic analysis. Low biomass microbiota samples (e.g. biopsies, tissue swabs and lavages) are receiving increasing attention, but optimal standardization for analysis of low biomass samples has yet to be developed. Here we tested the lower bacterial concentration required to perform 16S rRNA gene analysis using three different DNA extraction protocols, three different mechanical lysing series and two different PCR protocols. A mock microbiota community standard and low biomass samples (108, 107, 106, 105 and 104 microbes) from two healthy donor stools were employed to assess optimal sample processing for 16S rRNA gene analysis using paired-end Illumina MiSeq technology. Three DNA extraction protocols tested in our study performed similar with regards to representing microbiota composition, but extraction yield was better for silica columns compared to bead absorption and chemical precipitation. Furthermore, increasing mechanical lysing time and repetition did ameliorate the representation of bacterial composition. The most influential factor enabling appropriate representation of microbiota composition remains sample biomass. Indeed, bacterial densities below 106 cells resulted in loss of sample identity based on cluster analysis for all tested protocols. Finally, we excluded DNA extraction bias using a genomic DNA standard, which revealed that a semi-nested PCR protocol represented microbiota composition better than classical PCR. Based on our results, starting material concentration is an important limiting factor, highlighting the need to adapt protocols for dealing with low biomass samples. Our study suggests that the use of prolonged mechanical lysing, silica membrane DNA isolation and a semi-nested PCR protocol improve the analysis of low biomass samples. Using the improved protocol we report a lower limit of 106 bacteria per sample for robust and reproducible microbiota analysis.

scholarly journals Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon

2018 ◽  
Author(s):  
Anna Cusco ◽  
Carlotta Catozzi ◽  
Joaquim Vines ◽  
Armand Sanchez ◽  
Olga Francino
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Full Length ◽  
23S Rrna ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Microbiota Composition ◽  
Staphylococcus Pseudintermedius ◽  
Mock Communities

Background: Profiling microbiome on low biomass samples is challenging for metagenomics since these samples are prone to present DNA from other sources, such as the host or the environment. The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. Here, we aim to assess long-amplicon PCR-based approaches for assigning taxonomy at the genus and species level. We use Nanopore sequencing with two different markers: full-length 16S rRNA (~1,500 bp) and the whole rrn operon (16S rRNA gene - ITS - 23S rRNA gene; 4,500 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities (HM-783D, Bei Resources; D6306, ZymoBIOMICS) and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION (Oxford Nanopore Technologies) using 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using WIMP workflow on EPI2ME (ONT) or Minimap2 software with rrn database. Results: Full-length 16S rRNA and the rrn operon retrieved the microbiota composition from the bacterial isolate, the mock communities and the complex skin samples, even at the genus and species level. For Staphylococcus pseudintermedius isolate, when using EPI2ME, the amplicons were assigned to the correct bacterial species in ~98% of the cases with rrn operon as the marker, and ~68% of the cases with 16S rRNA gene respectively. In both skin microbiota samples, we detected many species with an environmental origin. In chin, we found different Pseudomonas species in high abundance, whereas in the dorsal skin there were more taxa with lower abundances. Conclusions: Both full-length 16S rRNA and the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, rrn operon would be the best choice.

scholarly journals Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S-ITS-23S of the rrn operon

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1755 ◽  
Author(s):  
Anna Cuscó ◽  
Carlotta Catozzi ◽  
Joaquim Viñes ◽  
Armand Sanchez ◽  
Olga Francino
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genetic Marker ◽  
Species Level ◽  
Full Length ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Microbiota Composition ◽  
The 16S Rrna Gene ◽  
Mock Communities

Background: Profiling the microbiome of low-biomass samples is challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual approach is sequencing short regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. To achieve an increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low-biomass samples (dog skin). Nanopore sequencing was performed on MinION™ using the 1D PCR barcoding kit. Sequences were pre-processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the rrn operon were used to retrieve the microbiota composition of the samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct bacterial species in ~98% of the cases with the16S-ITS-23S genetic marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA gene represented better the abundances of a microbial community; whereas, 16S-ITS-23S obtained better resolution at the species level. Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. For an increased resolution at the species level, targeting the 16S-ITS-23S of the rrn operon would be the best choice.

A systematic review of the microbiota composition in various peri-implant conditions: data from 16S rRNA gene sequencing

2020 ◽  
Vol 117 ◽  
pp. 104776
Author(s):  
Fabiana de Melo ◽  
Fernanda Carpes Milanesi ◽  
Patrícia Daniela Melchiors Angst ◽  
Rui Vicente Oppermann
Keyword(s):  
Systematic Review ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Rrna Gene Sequencing

scholarly journals High occurrence of Mycoplasma suis infection in swine herds from non-technified farms in Mossoró, state of Rio Grande do Norte, Northeastern Brazil

2016 ◽  
Vol 25 (4) ◽  
pp. 414-417 ◽  
Author(s):  
Mariana Aparecida Toledo ◽  
Alexandro Iris Leite ◽  
Luiz Ricardo Gonçalves ◽  
Keyla Carstens Marques de Sousa ◽  
Renan Bressianini do Amaral ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rio Grande ◽  
Northeastern Brazil ◽  
Economic Losses ◽  
Rrna Gene ◽  
High Occurrence ◽  
Mycoplasma Suis ◽  
Swine Herds ◽  
The City

Abstract Mycoplasma suis, the etiological agent of swine hemoplasmosis, has been neglected in swine herds around the world. Swine hemoplasmosis is frequently associated with hemolytic anemia, disgalacty, infertility and immunosuppression, and it results in significant economic losses. This study investigates the occurrence of M. suis in non-technified swine herds in the northeastern region of Brazil using quantitative PCR (qPCR) based on the 16S rRNA gene. Between March and August 2013, blood samples from 147 swine were collected during slaughter in the city of Mossoró, state of Rio Grande do Norte, northeastern Brazil. One hundred and twelve samples (76.19%) were positive for M. suis by qPCR assays. The range of Cqs and quantification (copies of a M. suis-16S rRNA gene fragment/µL) was 20.86–37.89 and 1.64×101–6.64×107, respectively. One can conclude that M. suis infection have high occurrence (76,19%) in non-technified swine-rearing systems in Mossoró in the state of Rio Grande do Norte, Brazil.

scholarly journals Effect of commercially purified deoxynivalenol and zearalenone mycotoxins on microbial diversity of pig cecum contents

2021 ◽  
Vol 34 (2) ◽  
pp. 243-255
Author(s):  
Kondreddy Eswar Reddy ◽  
Minji Kim ◽  
Ki Hyun Kim ◽  
Sang Yun Ji ◽  
Youlchang Baek ◽  
...  
Keyword(s):  
Immune Response ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gut Microbiome ◽  
Intestinal Microflora ◽  
Bacterial Flora ◽  
Economic Losses ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Bacterial 16S Rrna Gene

Objective: Deoxynivalenol (DON) and zearalenone (ZEN) are mycotoxins that frequently contaminate maize and grain cereals, imposing risks to the health of both humans and animals and leading to economic losses. The gut microbiome has been shown to help combat the effects of such toxins, with certain microorganisms reported to contribute significantly to the detoxification process.Methods: We examined the cecum contents of three different dietary groups of pigs (control, as well as diets contaminated with 8 mg DON/kg feed or 0.8 mg ZEN/kg feed). Bacterial 16S rRNA gene amplicons were acquired from the cecum contents and evaluated by next-generation sequencing.Results: A total of 2,539,288 sequences were generated with ~500 nucleotide read lengths. Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla, occupying more than 96% of all three groups. <i>Lactobacillus, Bacteroides, Megasphaera</i>, and <i>Campylobacter</i> showed potential as biomarkers for each group. Particularly, <i>Lactobacillus</i> and <i>Bacteroides</i> were more abundant in the DON and ZEN groups than in the control. Additionally, 52,414 operational taxonomic units were detected in the three groups; those of <i>Bacteroides, Lactobacillus, Campylobacter</i>, and <i>Prevotella</i> were most dominant and significantly varied between groups. Hence, contamination of feed by DON and ZEN affected the cecum microbiota, while <i>Lactobacillus</i> and <i>Bacteroides</i> were highly abundant and positively influenced the host physiology.Conclusion: <i>Lactobacillus</i> and <i>Bacteroides</i> play key roles in the process of detoxification and improving the immune response. We, therefore, believe that these results may be useful for determining whether disturbances in the intestinal microflora, such as the toxic effects of DON and ZEN, can be treated by modulating the intestinal bacterial flora.

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