scholarly journals Culture-Independent Characterization of the Digestive-Tract Microbiota of the Medicinal Leech Reveals a Tripartite Symbiosis

2006 ◽  
Vol 72 (7) ◽  
pp. 4775-4781 ◽  
Author(s):  
Paul L. Worthen ◽  
Cindy J. Gode ◽  
Joerg Graf
Keyword(s):  
Bacterial Community ◽  
Digestive Tract ◽  
Medicinal Leech ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Data Set ◽  
Clone Libraries ◽  
Host Interactions ◽  
Aeromonas Veronii ◽  
Culture Independent

ABSTRACT Culture-based studies of the microbial community within the gut of the medicinal leech have typically been focused on various Aeromonas species, which were believed to be the sole symbiont of the leech digestive tract. In this study, analysis of 16S rRNA gene clone libraries confirmed the presence of Aeromonas veronii and revealed a second symbiont, clone PW3, a novel member of the Rikenellaceae, within the crop, a large compartment where ingested blood is stored prior to digestion. The diversity of the bacterial community in the leech intestinum was determined, and additional symbionts were detected, including members of the α-, γ-, and δ-Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes. The relative abundances of the clones suggested that A. veronii and the novel clone, PW3, also dominate the intestinum community, while other clones, representing transient organisms, were typically present in low numbers. The identities of these transients varied greatly between individual leeches. Neither time after feeding nor feeding on defibrinated blood caused a change in identity of the dominant members of the microbial communities. Terminal restriction fragment length polymorphism analysis was used to verify that the results from the clone libraries were representative of a larger data set. The presence of a two-member bacterial community in the crop provides a unique opportunity to investigate both symbiont-symbiont and symbiont-host interactions in a natural model of digestive-tract associations.

scholarly journals The bacterial community of the lone star tick (Amblyomma americanum)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
L. Paulina Maldonado-Ruiz ◽  
Saraswoti Neupane ◽  
Yoonseong Park ◽  
Ludek Zurek
Keyword(s):  
Bacterial Community ◽  
Amblyomma Americanum ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Core Microbiome ◽  
Lone Star Tick ◽  
Animal Pathogens ◽  
Wide Range ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low. Methods We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks. Results We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin. Conclusions No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.

scholarly journals Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere

2010 ◽  
Vol 76 (24) ◽  
pp. 8117-8125 ◽  
Author(s):  
Paul J. Hunter ◽  
Paul Hand ◽  
David Pink ◽  
John M. Whipps ◽  
Gary D. Bending
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Population Diversity ◽  
Microbial Interactions ◽  
Soluble Carbohydrates ◽  
Rrna Gene ◽  
Species Variation ◽  
Clone Libraries ◽  
Microbe Interactions

ABSTRACT Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.

scholarly journals Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Luis M. Rodriguez-R ◽  
Santosh Gunturu ◽  
James M. Tiedje ◽  
James R. Cole ◽  
Konstantinos T. Konstantinidis
Keyword(s):  
Microbial Community ◽  
Shannon Index ◽  
Sequence Diversity ◽  
Metagenomic Data ◽  
Reference Database ◽  
Rrna Gene ◽  
Data Sets ◽  
Data Set ◽  
Genomic Study ◽  
Culture Independent

ABSTRACT Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies. Here, we extend Nonpareil, a database-independent tool for the estimation of coverage in metagenomic data sets, to a high-performance computing implementation that scales up to hundreds of cores and includes, in addition, a k -mer-based estimation as sensitive as the original alignment-based version but about three hundred times as fast. Further, we propose a metric of sequence diversity ( N d ) derived directly from Nonpareil curves that correlates well with alpha diversity assessed by traditional metrics. We use this metric in different experiments demonstrating the correlation with the Shannon index estimated on 16S rRNA gene profiles and show that N d additionally reveals seasonal patterns in marine samples that are not captured by the Shannon index and more precise rankings of the magnitude of diversity of microbial communities in different habitats. Therefore, the new version of Nonpareil, called Nonpareil 3, advances the toolbox for metagenomic analyses of microbiomes. IMPORTANCE Estimation of the coverage provided by a metagenomic data set, i.e., what fraction of the microbial community was sampled by DNA sequencing, represents an essential first step of every culture-independent genomic study that aims to robustly assess the sequence diversity present in a sample. However, estimation of coverage remains elusive because of several technical limitations associated with high computational requirements and limiting statistical approaches to quantify diversity. Here we described Nonpareil 3, a new bioinformatics algorithm that circumvents several of these limitations and thus can facilitate culture-independent studies in clinical or environmental settings, independent of the sequencing platform employed. In addition, we present a new metric of sequence diversity based on rarefied coverage and demonstrate its use in communities from diverse ecosystems.

scholarly journals Characterization of the Digestive-Tract Microbiota of Hirudo orientalis, a European Medicinal Leech

2008 ◽  
Vol 74 (19) ◽  
pp. 6151-6154 ◽  
Author(s):  
Alison S. Laufer ◽  
Mark E. Siddall ◽  
Joerg Graf
Keyword(s):  
Digestive Tract ◽  
Bacterial Infections ◽  
Medicinal Leech ◽  
Culture Independent ◽  
Hirudo Verbana ◽  
Culture Dependent

ABSTRACT FDA-approved, postoperative use of leeches can lead to bacterial infections. In this study, we used culture-dependent and culture-independent approaches to characterize the digestive-tract microbiota of Hirudo orientalis. Surprisingly, two Aeromonas species, A. veronii and A. jandaei, were cultured. Uncultured Rikenella-like bacteria were most similar to isolates from Hirudo verbana.

scholarly journals Most of the Dominant Members of Amphibian Skin Bacterial Communities Can Be Readily Cultured

2015 ◽  
Vol 81 (19) ◽  
pp. 6589-6600 ◽  
Author(s):  
Jenifer B. Walke ◽  
Matthew H. Becker ◽  
Myra C. Hughey ◽  
Meredith C. Swartwout ◽  
Roderick V. Jensen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Batrachochytrium Dendrobatidis ◽  
Amplicon Sequencing ◽  
Reference Database ◽  
Rrna Gene ◽  
Amphibian Skin ◽  
Amphibian Species ◽  
Content Type ◽  
Average Percentage ◽  
Culture Independent

ABSTRACTCurrently, it is estimated that only 0.001% to 15% of bacteria in any given system can be cultured by use of commonly used techniques and media, yet culturing is critically important for investigations of bacterial function. Despite this situation, few studies have attempted to link culture-dependent and culture-independent data for a single system to better understand which members of the microbial community are readily cultured. In amphibians, some cutaneous bacterial symbionts can inhibit establishment and growth of the fungal pathogenBatrachochytrium dendrobatidis, and thus there is great interest in using these symbionts as probiotics for the conservation of amphibians threatened byB. dendrobatidis. The present study examined the portion of the culture-independent bacterial community (based on Illumina amplicon sequencing of the 16S rRNA gene) that was cultured with R2A low-nutrient agar and whether the cultured bacteria represented rare or dominant members of the community in the following four amphibian species: bullfrogs (Lithobates catesbeianus), eastern newts (Notophthalmus viridescens), spring peepers (Pseudacris crucifer), and American toads (Anaxyrus americanus). To determine which percentage of the community was cultured, we clustered Illumina sequences at 97% similarity, using the culture sequences as a reference database. For each amphibian species, we cultured, on average, 0.59% to 1.12% of each individual's bacterial community. However, the average percentage of bacteria that were culturable for each amphibian species was higher, with averages ranging from 2.81% to 7.47%. Furthermore, most of the dominant operational taxonomic units (OTUs), families, and phyla were represented in our cultures. These results open up new research avenues for understanding the functional roles of these dominant bacteria in host health.

Roles of Oligotrophic Acidophiles (Alicyclobacillus) in Chalcopyrite Bioleaching System: Shake Flask Evaluation

2015 ◽  
Vol 1130 ◽  
pp. 410-413
Author(s):  
Xing Yu Liu ◽  
Ming Jiang Zhang ◽  
Wen Yan Liu ◽  
Bo Wei Chen ◽  
Chun Yu Meng ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Mine Drainage ◽  
Community Change ◽  
Rrna Gene ◽  
Acid Mine ◽  
Copper Leaching ◽  
Culture Independent ◽  
Different Temperatures ◽  
Two Temperatures

An oligotrophic culture of acidophiles (Alicyclobacillus) isolated from Dexin acid mine drainage was evaluated for its synergistic effect in chalcopyrite bioleaching. Bioleaching of chalcopyrite with and without theAlicyclobacillusculture was investigated at different temperatures (33°C, 45 °C and 65 °C) and a culture-independent approach based on 16S rRNA gene clone library was used to analyze changes in the microbial community change during the bioleaching process. For 33oC leaching tests, only the bacterial community was analyzed, but for the other two temperatures, both the bacterial community and archaea communities were analyzed. Results showed that at high leaching temperature (65°C),Alicyclobacillusculture could increase copper leaching recovery from 57.83% to 60.7%. While at relative low temperature (45°C and 33°C), addingAlicyclobacillusculture inhibited copper bioleaching, copper leaching recovery decreased from 36.10% to 31.52% and from 34.02% to 21.97% respectively at 45°C and 33°C. Clone libraries analysis showed thatAlicyclobacillushelps the growth of genusSulfobacillusat 45 °C while inhibiting the growth of genusLeptospillumat both 33°C and 45 °C. Furthermore, when addingAlicyclobacillusgrowth ofFerroplasmawas limited andAcidoplasmawas facilitated at 45°C. At 60°C, addingAlicyclobacillusculture facilitated the growth of genusMetallosphaerawhile limiting the growth ofLeptospillumandFerroplasma. The results showed potential application ofAlicyclobacillusin high temperature chalcopyrite bioleaching and bioremediation of acid mine drainage.

scholarly journals Soil and Rhizosphere Bacterial Diversity in Maize Agro- Ecosystem

2017 ◽  
Vol 6 (3) ◽  
pp. 35 ◽  
Author(s):  
Maria Teresa Federici Rodriguez ◽  
Natalia Bajsa Valverde ◽  
Paula Lagurara ◽  
Santiago Revale ◽  
Jackson Antonio Marcondes de Souza ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Management Practices ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Community Diversity ◽  
Rrna Gene ◽  
Phenological Stages ◽  
Maize Production ◽  
Maize Cultivars ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

Management practices used in maize production have an impact on soil agro- ecosystems where different microbial communities coexist. Soil inhabiting bacteria are numerous and diverse, but we know very little about their ecological distribution. Here we analyzed the bacterial community diversity in the rhizosphere of two transgenic maize cultivars, in agricultural soil before sowing and in non-cultivated soil in an experimental site in the south region of Uruguay. We followed two culture-independent methods: DGGE (denaturing gradient gel electrophoresis) and 454-pyrosequencing of 16S rRNA gene amplicon. Through pyrosequencing, the three environments analyzed presented differences in terms of bacterial composition. However, no differences were found in the relative abundance of the ten most represented phyla in the rhizosphere of the two cultivars at different phenological stages. We found significant differences of Bacteroidetes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia phyla when comparing agricultural and non-cultivated soils, as well as a significant enrichment of members of the phylum Gemmatimonadetes in all rhizosphere samples compared to soil. Through DGGE analysis we evidenced that maize rhizosphere bacterial communities changed at different phenological stages in both cultivars. We also provided baseline information about bacterial specific taxa within maize agro- ecosystem for further evaluation of possible rhizosphere bacterial community shifts of genetically modified maize cultivars under different management practices.

scholarly journals Spatial and Temporal Population Dynamics of a Naturally Occurring Two-Species Microbial Community inside the Digestive Tract of the Medicinal Leech

2007 ◽  
Vol 73 (6) ◽  
pp. 1984-1991 ◽  
Author(s):  
Yoshitomo Kikuchi ◽  
Joerg Graf
Keyword(s):  
Population Dynamics ◽  
Digestive Tract ◽  
Bacterial Species ◽  
Single Species ◽  
Medicinal Leech ◽  
Aeromonas Veronii ◽  
Lectin Staining ◽  
Naturally Occurring ◽  
Hirudo Verbana

ABSTRACT The medicinal leech, Hirudo verbana, is one of the simplest naturally occurring models for digestive-tract symbioses, where only two bacterial species, Aeromonas veronii bv. sobria (γ-Proteobacteria) and a Rikenella-like bacterium (Bacteroidetes), colonize the crop, the largest compartment of the leech digestive tract. In this study, we investigated spatial and temporal changes of the localization and microcolony structure of the native symbionts in the crop, after ingestion of a sterile blood meal, by fluorescence in situ hybridization. The population dynamics differed between the two symbiotic bacteria. A. veronii was detected mainly as individual cells inside the intraluminal fluid (ILF) during 14 days after feeding (daf) unless it was found in association with Rikenella microcolonies. The Rikenella-like bacteria were observed not only inside the ILF but also in association with the luminal surface of the crop epithelium. The sizes of Rikenella microcolonies changed dynamically through the 14-day period. From 3 daf onward, mixed microcolonies containing both species were frequently observed, with cells of both species tightly associating with each other. The sizes of the mixed microcolonies were consistently larger than the size of either single-species microcolony, suggesting a synergistic interaction of the symbionts. Lectin staining with succinylated wheat germ agglutinin revealed that the planktonic microcolonies present in the ILF were embedded in a polysaccharide matrix containing N-acetylglucosamine. The simplicity, symbiont-symbiont interaction, and mixed microcolonies of this naturally occurring, digestive-tract symbiosis lay the foundation for understanding the more complex communities residing in most animals.

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