16S rRNA profiling of the dermatophagoides farinae core microbiome: Enterococcus and bartonella

ABSTRACT Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animals.

Download Full-text

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato

Environmental Microbiome ◽

10.1186/s40793-020-00364-9 ◽

2020 ◽

Vol 15 (1) ◽

Author(s):

Peter Kusstatscher ◽

Wisnu Adi Wicaksono ◽

Alessandro Bergna ◽

Tomislav Cernava ◽

Nick Bergau ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Statistical Tests ◽

Central Element ◽

Shannon Index ◽

Gene Copy ◽

Rrna Gene ◽

Core Microbiome ◽

Defense Strategies

Abstract Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments. Results Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108–109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed. Conclusion Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.

Download Full-text

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

Scientific Reports ◽

10.1038/s41598-019-53769-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 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.

Download Full-text

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato

10.21203/rs.3.rs-25108/v1 ◽

2020 ◽

Author(s):

Peter Kusstatscher ◽

Wisnu Adi Wicaksono ◽

Alessandro Bergna ◽

Tomislav Cernava ◽

Nick Bergau ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Dynamics ◽

Statistical Tests ◽

Central Element ◽

Shannon Index ◽

Gene Copy ◽

Rrna Gene ◽

Core Microbiome ◽

Defense Strategies

Abstract Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments.Results Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108- 109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific taxa; Burkholderiaceae and Actinobacteria showed similar pattern. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed.Conclusion Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.

Download Full-text

Methanogenic Granules Are Replicated, Whole Microbial Communities With Reproducible Responses To Environmental Cues

10.21203/rs.3.rs-16883/v1 ◽

2020 ◽

Author(s):

Anna Christine Trego ◽

Sarah O'Sullivan ◽

Simon Mills ◽

Estefania Porca ◽

Christopher Quince ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Size Fraction ◽

Methanogenic Archaea ◽

Organic Content ◽

Environmental Cues ◽

Rrna Gene ◽

Core Microbiome ◽

Methanogenic Activity ◽

Fermentative Bacteria

Abstract Background In this study, individual anaerobic granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates originated from three different biomass sources, i.e. three different engineered biological wastewater treatment systems, were each size-separated into three fractions – small, medium and large – and characterised according to organic matter concentrations and rates of methanogenic activity. Differences in the microbial community structure of each size fraction from each source were determined using 16S rRNA gene sequencing. Subsequently, single granules from the large size fraction of one of the sources were separately subjected controlled environmental cues in novel micro batch reactors (mBRs). Results Organic content, methanogenic activity, and microbial community were significantly different between the three size fractions, with diversity trajectories replicated across the three sludge sources – indicating a potential development model as granules age. Individual large granules from one of these sources were statistically identical with respect to the structure of the active community based on cDNA analysis. It was observed that the active microbial community of individual granules, at the depth of 16S rRNA sequencing, produced reproducible responses to environmental conditions. While each condition resulted in the up-regulation of particular OTUs and clades, the core microbiome, consisting of many fermentative bacteria along with methanogenic archaea, namely, Methanosarcina and Methanobacterium , persisted. Conclusions At this level, single anaerobic granules can be considered highly-replicated whole-ecosystems, opening the door to high-throughput studies in Microbial Ecology.

Download Full-text

16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates

PeerJ ◽

10.7717/peerj.8417 ◽

2020 ◽

Vol 8 ◽

pp. e8417 ◽

Cited By ~ 2

Author(s):

Qiang Chen ◽

William A. Meyer ◽

Qiuwei Zhang ◽

James F. White

Keyword(s):

Microbial Community ◽

Seed Germination ◽

Bacterial Community ◽

16S Rrna ◽

Seedling Growth ◽

Bacterial Communities ◽

Metagenomic Analysis ◽

High Moisture ◽

Core Microbiome ◽

Dry Climates

Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth.

Download Full-text

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the 16S rRNA gene

10.7287/peerj.preprints.1269v1 ◽

2015 ◽

Author(s):

Hans Verstraelen ◽

Ramiro Vilchez-Vargas ◽

Fabian Desimpel ◽

Ruy Jauregui ◽

Nele Vankeirsbilck ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Pregnant Women ◽

Deep Sequencing ◽

Human Reproduction ◽

Rrna Gene ◽

Ribosomal Database Project ◽

Core Microbiome ◽

Uterine Anomalies ◽

The 16S Rrna Gene

Background. It is widely assumed that the uterine cavity in non-pregnant women is a sterile body environment under physiological conditions. We have previously shown that some women with overt dysbiosis of the vaginal microbiome, present with a polymicrobial Gardnerella vaginalis-dominated covering the endometrium, casting doubt over the paradigm of the sterilityof the human uterus. We therefore aimed to assess the putative presence of a uterine microbiome in a series of non-pregnant women through deep sequencing of the V1-2 hypervariable region of the 16S ribosomal RNA (rRNA) gene. Methods. We sampled the endometrial surface by use of a transcervical device designed to avoid contamination from the vagina and endocervix in nineteen non-pregnant women with reproductive failure in the absence of uterine anomalies on hysteroscopy. Following DNA extraction, the V1-2 region of the 16S rRNA gene was targeted using the 27F and 338R primers. By use of the Illumina MiSeq platform, 16S rRNA gene amplicon sequences were identified and annotated by use of the Ribosomal Database Project. Results. Out of 183 unique 16S rRNA gene amplicon sequences, 15 operational taxonomic units or phylotypes were present in all samples, possibly representing the uterine core microbiome, dominated by Bacteroides xylanivorans, Bacteroides thetaiotaomicron, Bacteroides fragilis, and Pelomonas. Accordingly, three bacterial phyla, Proteobacteria, Firmicutes and Bacteroidetes, were consistently present. In some women, the endometrial community was also characterized by a single abundant species co-occurring with the core microbiota, in particular Lactobacillus crispatus, Lactobacillus iners, and Prevotella amnii, while in two women the community was largely different. Discussion. Our findings are, albeit not necessarily generalizable, consistent with the presence of a unique microbiome residing on the endometrium of the human non-pregnant uterus in women of reproductive age. A majority of women showed a rather similar endometrial community, dominated by only a few Bacteroides and Pelomonas phylotypes. Consistent with our current understanding of the human microbiome, the uterine microbiome is likely to have a previously unrecognized role in uterine physiology and human reproduction. Further study is therefore warranted to document community ecology and dynamics of the uterine microbiota, as well as the role of the uterine microbiome in health and disease.

Download Full-text

Influence of 16S rRNA Reference Databases in Amplicon-Based Environmental Microbiome Research

10.21203/rs.3.rs-961238/v1 ◽

2021 ◽

Author(s):

Meganathan P. Ramakodi

Keyword(s):

16S Rrna ◽

Reference Database ◽

P Value ◽

Ribosomal Database Project ◽

Core Microbiome ◽

Microbiome Composition ◽

Common Reference ◽

Microbiome Research ◽

Reference Databases ◽

The Impact

Abstract Purpose: The reference databases play a pivotal role in amplicon microbiome research but the sequence content and taxonomic information available in common reference databases differ. Studies on mock community and human health microbiome have revealed the problems associated with the choice of reference database on the outcome. Nonetheless, the influence of reference databases in environmental microbiome studies is not explicitly illustrated. Methods: This study analyzed the amplicon (V1V3, V3V4, V4V5 and V6V8) data of 128 soil samples and evaluated the impact of 16S rRNA databases, Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA and Consensus Taxonomy (ConTax), on microbiome inference. Results: The analyses showed that the distribution of observed amplicon sequence variants was significantly different (P-value < 2.647e-12) across four datasets, generated based on different databases for each amplicon region. In addition, the beta diversity was also found to be altered by different databases. Further investigation revealed that the microbiome composition inferred by different databases vary significantly (P-value=0.001), irrespective of amplicon regions. Importantly, the study found that the core-microbiome structure in environmental studies could be altered by the reference databases. Conclusion: In summary, this present study illustrates that the choice of reference database could influence the outcome of environmental microbiome research.

Download Full-text

Assessing the impact of dental and periodontal statuses on the salivary microbiome: a global oral health scale

10.1101/2020.05.16.20104190 ◽

2020 ◽

Author(s):

Marta Relvas ◽

Alba Regueira-Iglesias ◽

Carlos Balsa-Castro ◽

Filomena Salazar ◽

Jose Julio Pacheco ◽

...

Keyword(s):

Oral Health ◽

Bacterial Community ◽

16S Rrna ◽

Oral Disease ◽

Rrna Gene ◽

Convenience Sample ◽

Core Microbiome ◽

Rdna Sequencing ◽

Salivary Microbiota ◽

The Impact

Very few 16S rRNA-based studies have conducted a simultaneous analysis to identify the impact of various dental and periodontal parameters and determine which of them have the greatest repercussion for the salivary microbiota. Consequently, this study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental, periodontal and global oral disease. Our global oral health scale was used to produce a convenience sample of 81 patients from 270 who were initially recruited. These subjects were assigned the following grades: 47 had a periodontal grade (PG) of 0 and dental grades (DGs) between 0-3, and 46 had a DG of 0 and PGs between 0-3. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 x 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the Phyloseq, DESeq2 and Microbiome packages. The impact on the salivary microbiota of the different DGs, PGs and global oral grades (GGs) was investigated in relation to: 1) indicators of alpha diversity and the structure of the bacterial community; and 2) the composition of the core microbiome and the results of differential abundance tests. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or global oral disease, especially in high grades. The non-specific microbiome core contains a greater number of more abundant species than the specific core of a particular dental or periodontal condition (health or pathology). The number of taxa in the salivary microbiota with differential abundances between the DGs, PGs or GGs represents, at most, a quarter of the bacterial community and are mainly non-core species. Supragingival dental parameters influence the microbiota`s abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that global oral health has on salivary microbiome.

Download Full-text