scholarly journals Metagenomics Analysis Reveals an Extraordinary Inner Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae

2021 ◽  
Vol 9 (5) ◽  
pp. 1088
Author(s):  
Susana C. Arcos ◽  
Felipe Lira ◽  
Lee Robertson ◽  
María Rosa González ◽  
Noelia Carballeda-Sangiao ◽  
...  
Keyword(s):  
Diversity Indices ◽  
Rrna Gene ◽  
Clinical Effects ◽  
Associated Bacteria ◽  
Fresh Fish ◽  
Operational Taxonomic Units ◽  
Fish Hosts ◽  
Fishing Area ◽  
Anisakid Nematodes

L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as infectious agents causing allergies and as potential vectors of pathogens and microrganisms. In spite of the close bacteria–nematode relationship very little is known of the anisakids microbiota. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of anisakids when the L3 larvae migrate through the muscles. As a consequence, the bacterial inoculum will be spread, with potential effects on the quality of the fish, and possible clinical effects cannot be discarded. A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 fishing area were studied. Bacteria were taxonomically characterized through 1803 representative operational taxonomic units (OTUs) sequences. Fourteen phyla, 31 classes, 52 orders, 129 families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity indices (Shannon and Simpson) indicate an extraordinary diversity of bacteria at an OTU level. There are clusters of anisakids individuals (samples) defined by the associated bacteria which, however, are not significantly related to fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of anisakids taxa has to be expressed by the association among bacterial OTUs or other taxonomical levels which range from OTUs to the phylum level. There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from phylum to genus level, which could also be an indicator of fish contamination or the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for defining such structures.

scholarly journals Metagenomics Analysis Reveals An Extraordinary Bacterial Diversity in Anisakids (Nematoda: Anisakidae) L3 Larvae

2020 ◽  
Author(s):  
Susana C. Arcos ◽  
Felipe Lira ◽  
Lee Robertson ◽  
María Rosa González ◽  
Noelia Carballeda-Sangiao ◽  
...  
Keyword(s):  
Diversity Indices ◽  
Rrna Gene ◽  
Clinical Effects ◽  
16S Rrna Gene Sequences ◽  
Associated Bacteria ◽  
Fresh Fish ◽  
Bacterial Inoculum ◽  
Fish Hosts ◽  
Anisakid Nematodes

Abstract Background: L3 larvae of anisakid nematodes are an important problem for the fisheries industry and pose a potential risk for human health by acting as agents causing allergies and as potential vectors of pathogens microrganisms. In spite of the close bacteria-nematode relationship very little is known of the Anisakids microbiote. Fresh fish could be contaminated by bacteria vectored in the cuticle or in the intestine of Anisakids when the L3 larvae migrate through the muscles. As a consequence the bacterial inoculum will be spread, affecting the quality of the fish, and possible clinical effects cannot be discardedResults: A total of 2,689,113 16S rRNA gene sequences from a total of 113 L3 individuals obtained from fish captured along the FAO 27 area were studied. Bacteria were taxonomically characterized through 1803 representative OTUsequences. Fourteen Phyla, 31 Classes, 52 Orders, 129 Families and 187 genera were unambiguously identified. We have found as part of microbiome an average of 123 OTUs per L3 individual. Diversity Indices (Shannon and Simpson indices) indicate an extraordinary diversity of bacteria at a OTU level. There are clusters of Anisakids individuals (samples) defined by the associated bacteria which however are not significantly related with fish hosts or anisakid taxa. This suggests that association or relationship among bacteria in Anisakids, exists without the influence of fishes or nematodes. The lack of relationships with hosts of Anisakids taxa has to be necessarily expresssed by the association among bacterial OTUs or other taxonomical levels which are ranging from OTUs to phylum level. Conclusions: There are significant biological structural associations of microbiota in anisakid nematodes which manifest in clusters of bacteria ranging from plyllum to genus level which could also be anindicator of degree of fish contamination or from the geographic zone of fish capture. Actinobacteria, Aquificae, Firmicutes, and Proteobacteria are the phyla whose abundance value discriminate for difining such structures.

Variation in the microbiome of the spider mite Tetranychus truncatus with sex, instar and endosymbiont infection

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Yu-Xi Zhu ◽  
Zhang-Rong Song ◽  
Shi-Mei Huo ◽  
Kun Yang ◽  
Xiao-Yue Hong
Keyword(s):  
Spider Mite ◽  
Potential Role ◽  
Developmental Stages ◽  
Spider Mites ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Operational Taxonomic Units ◽  
Dominant Bacteria ◽  
The 16S Rrna Gene

ABSTRACT Most arthropod-associated bacterial communities play a crucial role in host functional traits, whose structure could be dominated by endosymbionts. The spider mite Tetranychus truncatus is a notorious agricultural pest harboring various endosymbionts, yet the effects of endosymbionts on spider mite microbiota remain largely unknown. Here, using deep sequencing of the 16S rRNA gene, we characterized the microbiota of male and female T. truncatus with different endosymbionts (Wolbachia and Spiroplasma) across different developmental stages. Although the spider mite microbiota composition varied across the different developmental stages, Proteobacteria were the most dominant bacteria harbored in all samples. Positive relationships among related operational taxonomic units dominated the significant coassociation networks among bacteria. Moreover, the spider mites coinfected with Wolbachia and Spiroplasma had a significantly higher daily fecundity and juvenile survival rate than the singly infected or uninfected spider mites. The possible function of spider-mite associated bacteria was discussed. Our results highlight the dynamics of spider mite microbiotas across different life stages, and the potential role of endosymbionts in shaping the microbiota of spider mites and improving host fitness.

scholarly journals OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units

2016 ◽  
Author(s):  
Sarah L. Westcott ◽  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Significant Advance ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Operational Taxonomic Units ◽  
Computational Bottleneck

AbstractAssignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to ten other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6-times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the dataset. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications.

scholarly journals Application of database-independent approach to assess the quality of OTU picking methods

2016 ◽  
Author(s):  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
Clustering Algorithms ◽  
Reference Database ◽  
Rrna Gene ◽  
Robust Method ◽  
16S Rrna Gene Sequences ◽  
Bacterial Taxonomy ◽  
Operational Taxonomic Units ◽  
Matthew’S Correlation Coefficient

AbstractAssigning 16S rRNA gene sequences to operational taxonomic units (OTUs) allows microbial ecologists to overcome the inconsistencies and biases within bacterial taxonomy and provides a strategy for clustering similar sequences that do not have representatives in a reference database. I have applied the Matthew’s correlation coefficient to assess the ability of 15 reference-independent and ‐dependent clustering algorithms to assign sequences to OTUs. This metric quantifies the ability of an algorithm to reflect the relationships between sequences without the use of a reference and can be applied to any dataset or method. The most consistently robust method was the average neighbor algorithm; however, for some datasets other algorithms matched its performance.

scholarly journals OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

mSphere ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Sarah L. Westcott ◽  
Patrick D. Schloss
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Significant Advance ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Operational Taxonomic Units ◽  
Taxonomic Groups

ABSTRACT Assignment of 16S rRNA gene sequences to operational taxonomic units (OTUs) is a computational bottleneck in the process of analyzing microbial communities. Although this has been an active area of research, it has been difficult to overcome the time and memory demands while improving the quality of the OTU assignments. Here, we developed a new OTU assignment algorithm that iteratively reassigns sequences to new OTUs to optimize the Matthews correlation coefficient (MCC), a measure of the quality of OTU assignments. To assess the new algorithm, OptiClust, we compared it to 10 other algorithms using 16S rRNA gene sequences from two simulated and four natural communities. Using the OptiClust algorithm, the MCC values averaged 15.2 and 16.5% higher than the OTUs generated when we used the average neighbor and distance-based greedy clustering with VSEARCH, respectively. Furthermore, on average, OptiClust was 94.6 times faster than the average neighbor algorithm and just as fast as distance-based greedy clustering with VSEARCH. An empirical analysis of the efficiency of the algorithms showed that the time and memory required to perform the algorithm scaled quadratically with the number of unique sequences in the data set. The significant improvement in the quality of the OTU assignments over previously existing methods will significantly enhance downstream analysis by limiting the splitting of similar sequences into separate OTUs and merging of dissimilar sequences into the same OTU. The development of the OptiClust algorithm represents a significant advance that is likely to have numerous other applications. IMPORTANCE The analysis of microbial communities from diverse environments using 16S rRNA gene sequencing has expanded our knowledge of the biogeography of microorganisms. An important step in this analysis is the assignment of sequences into taxonomic groups based on their similarity to sequences in a database or based on their similarity to each other, irrespective of a database. In this study, we present a new algorithm for the latter approach. The algorithm, OptiClust, seeks to optimize a metric of assignment quality by shuffling sequences between taxonomic groups. We found that OptiClust produces more robust assignments and does so in a rapid and memory-efficient manner. This advance will allow for a more robust analysis of microbial communities and the factors that shape them. Podcast: A podcast concerning this article is available.

scholarly journals PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and 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. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

scholarly journals Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

2020 ◽  
Vol 30 (1) ◽  
Author(s):  
Rashid Pervez ◽  
Showkat Ahmad Lone ◽  
Sasmita Pattnaik
Keyword(s):  
Insect Pests ◽  
Entomopathogenic Nematode ◽  
Alcaligenes Faecalis ◽  
Symbiotic Bacteria ◽  
Rrna Gene ◽  
Main Body ◽  
Associated Bacteria ◽  
Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

scholarly journals Comparison of Microbiological Characteristics and Genetic Diversity between Burkholderia cepacia Complex Isolates from Vascular Access and Other Clinical Infections

2020 ◽  
Vol 9 (1) ◽  
pp. 51
Author(s):  
Min Yi Wong ◽  
Yuan-Hsi Tseng ◽  
Tsung-Yu Huang ◽  
Bor-Shyh Lin ◽  
Chun-Wu Tung ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Vascular Access ◽  
Burkholderia Cepacia ◽  
Bacterial Species ◽  
Diversity Indices ◽  
Burkholderia Cepacia Complex ◽  
Reca Gene ◽  
Clinical Effects ◽  
Environmental Distribution ◽  
Microbiological Characteristics

Burkholderia cepacia complex (BCC) is a group of closely related bacteria with widespread environmental distribution. BCC bacteria are opportunistic pathogens that cause nosocomial infections in patients, especially cystic fibrosis (CF). Multilocus sequence typing (MLST) is used nowadays to differentiate species within the BCC complex. This study collected 41 BCC isolates from vascular access infections (VAIs) and other clinical infections between 2014 and 2020. We preliminarily identified bacterial isolates using standard biochemical procedures and further conducted recA gene sequencing and MLST for species identification. We determined genetic diversity indices using bioinformatics software. We studied 14 isolates retrieved from patients with VAIs and observed that Burkholderia cepacia was the predominant bacterial species, and B. contaminans followed by B. cenocepacia were mainly retrieved from patients with other infections. According to MLST data, we identified that all B. contaminans isolates belonged to ST102, while a wide variety of sequence types (STs) were found in B. cenocepacia isolates. In summary, the high diversity and easy transmission of BCC increase BCC infections, which provides insights into their potential clinical effects in non-CF infections.

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