scholarly journals Worldwide exploration of the microbiome harbored by the cnidarian model,Exaiptasia pallida(Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3235 ◽  
Author(s):  
Tanya Brown ◽  
Christopher Otero ◽  
Alejandro Grajales ◽  
Estefania Rodriguez ◽  
Mauricio Rodriguez-Lanetty
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Species ◽  
Sea Anemone ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Wide Range ◽  
Exaiptasia Pallida

Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemoneExaiptasia pallidashows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated withE. pallidaare broadly conserved across geographic space with samples, containing largelyProteobacteriaandBacteroides.However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgalSymbiodiniumsymbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact thatE. pallidais likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone modelE. pallidais the first global-scale study of its kind.

scholarly journals Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank

2016 ◽  
Author(s):  
Tanya Brown ◽  
Christopher Otero ◽  
Alejandro Grajales ◽  
Estefania Rodriguez ◽  
Mauricio Rodriguez-Lanetty
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Species ◽  
Sea Anemone ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Wide Range ◽  
Exaiptasia Pallida

Examination of host-microbe interactions in basal metazoans, such as cnidarians is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V4 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. These results contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. Instead, our findings suggest that environmental settings, not host specificity seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.

scholarly journals Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank

2016 ◽  
Author(s):  
Tanya Brown ◽  
Christopher Otero ◽  
Alejandro Grajales ◽  
Estefania Rodriguez ◽  
Mauricio Rodriguez-Lanetty
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Species ◽  
Sea Anemone ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Wide Range ◽  
Exaiptasia Pallida

Examination of host-microbe interactions in basal metazoans, such as cnidarians is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V4 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. These results contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. Instead, our findings suggest that environmental settings, not host specificity seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.

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 Interaction between typical sulfonamides and bacterial diversity in drinking water

2018 ◽  
Vol 16 (6) ◽  
pp. 914-920 ◽  
Author(s):  
Qing Wu ◽  
Shuqun Li ◽  
Xiaofei Zhao ◽  
Xinhua Zhao
Keyword(s):  
Drinking Water ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Microbial Community Structure ◽  
Antibiotic Use ◽  
Community Diversity ◽  
Wide Range ◽  
Growth Of Bacteria

Abstract The abuse of antibiotics is becoming more serious as antibiotic use has increased. The sulfa antibiotics, sulfamerazine (SM1) and sulfamethoxazole (SMZ), are frequently detected in a wide range of environments. The interaction between SM1/SMZ and bacterial diversity in drinking water was investigated in this study. The results showed that after treatment with SM1 or SMZ at four different concentrations, the microbial community structure of the drinking water changed statistically significantly compared to the blank sample. At the genus level, the proportions of the different bacteria in drinking water may affect the degradation of the SM1/SMZ. The growth of bacteria in drinking water can be inhibited after the addition of SM1/SMZ, and bacterial community diversity in drinking water declined in this study. Furthermore, the resistance gene sul2 was induced by SM1 in the drinking water.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

scholarly journals Phytate and Microbial Suspension Amendments Increased Soybean Growth and Shifted Microbial Community Structure

2021 ◽  
Vol 9 (9) ◽  
pp. 1803
Author(s):  
Bulbul Ahmed ◽  
Jean-Baptiste Floc’h ◽  
Zakaria Lahrach ◽  
Mohamed Hijri
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Indicator Species ◽  
Mycorrhizal Fungi ◽  
Rrna Gene ◽  
Soybean Plant ◽  
Trichoderma Spp ◽  
Undisturbed Soil ◽  
Microbial Suspension

Phytate represents an organic pool of phosphorus in soil that requires hydrolysis by phytase enzymes produced by microorganisms prior to its bioavailability by plants. We tested the ability of a microbial suspension made from an old growth maple forest’s undisturbed soil to mineralize phytate in a greenhouse trial on soybean plants inoculated or non-inoculated with the suspension. MiSeq Amplicon sequencing targeting bacterial 16S rRNA gene and fungal ITS was performed to assess microbial community changes following treatments. Our results showed that soybean nodulation and shoot dry weight biomass increased when phytate was applied to the nutrient-poor substrate mixture. Bacterial and fungal diversities of the root and rhizosphere biotopes were relatively resilient following inoculation by microbial suspension; however, bacterial community structure was significantly influenced. Interestingly, four arbuscular mycorrhizal fungi (AMF) were identified as indicator species, including Glomus sp., Claroideoglomus etunicatum, Funneliformis mosseae and an unidentified AMF taxon. We also observed that an ericoid mycorrhizal taxon Sebacina sp. and three Trichoderma spp. were among indicator species. Non-pathogenic Planctobacteria members highly dominated the bacterial community as core and hub taxa for over 80% of all bacterial datasets in root and rhizosphere biotopes. Overall, our study documented that inoculation with a microbial suspension and phytate amendment improved soybean plant growth.

scholarly journals 16S rRNA Gene-Based Profiling of the Microbial Community in an Acid Mine Drainage Fe Precipitate at Libiola Mine (Liguria, Italy)

Minerals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1064
Author(s):  
Sirio Consani ◽  
Stefano Ghignone ◽  
Marina Pozzolini ◽  
Marco Giovine ◽  
Luigi Vezzulli ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Bacterial Species ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Acid Mine ◽  
Starting Point ◽  
Wide Range ◽  
Libiola Mine

Acid mine drainage (AMD) is a common environmental problem in many sulphide mines worldwide, and it is widely accepted that the microbial community plays a major role in keeping the process of acid generation active. The aim of this work is to describe, for the first time, the microbial community thriving in goethite and jarosite Fe precipitates from the AMD of the Libiola mine. The observed association is dominated by Proteobacteria (>50%), followed by Bacteroidetes (22.75%), Actinobacteria (7.13%), Acidobacteria (5.79%), Firmicutes (2.56%), and Nitrospirae (1.88%). Primary producers seem to be limited to macroalgae, with chemiolithotrophic strains being almost absent. A phylogenetic analysis of bacterial sequences highlighted the presence of heterotrophic bacteria, including genera actively involved in the AMD Fe cycle and genera (such as Cytophaga and Flavobacterium) that are able to reduce cellulose. The Fe precipitates constitute a microaerobic and complex environment in which many ecological niches are present, as proved by the wide range of bacterial species observed. This study is the first attempt to quantitatively characterize the microbial community of the studied area and constitutes a starting point to learn more about the microorganisms thriving in the AMD of the Libiola mine, as well as their potential applications.

scholarly journals Characteristics of bacterial community in cloud water at Mt Tai: similarity and disparity under polluted and non-polluted cloud episodes

2017 ◽  
Vol 17 (8) ◽  
pp. 5253-5270 ◽  
Author(s):  
Min Wei ◽  
Caihong Xu ◽  
Jianmin Chen ◽  
Chao Zhu ◽  
Jiarong Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Major Ions ◽  
Cloud Water ◽  
Rrna Gene ◽  
Bacterial Gene ◽  
Wide Range

Abstract. Bacteria are widely distributed in atmospheric aerosols and are indispensable components of clouds, playing an important role in the atmospheric hydrological cycle. However, limited information is available about the bacterial community structure and function, especially for the increasing air pollution in the North China Plain. Here, we present a comprehensive characterization of bacterial community composition, function, variation, and environmental influence for cloud water collected at Mt Tai from 24 July to 23 August 2014. Using Miseq 16S rRNA gene sequencing, the highly diverse bacterial community in cloud water and the predominant phyla of Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were investigated. Bacteria that survive at low temperature, radiation, and poor nutrient conditions were found in cloud water, suggesting adaption to an extreme environment. The bacterial gene functions predicted from the 16S rRNA gene using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that the pathways related to metabolism and disease infections were significantly correlated with the predominant genera. The abundant genera Acinetobacter, Stenotrophomonas, Pseudomonas, and Empedobacter originated from a wide range of habitats including cloud condensation nuclei and ice nuclei active species, opportunistic pathogens, and functional species, demonstrating the importance of ecology and health in cloud water. Cluster analysis including hierarchical cluster (Hcluster) and principal coordinate analysis (PCoA) indicated a significant disparity between polluted and non-polluted samples. Linear discriminant analysis effect size (LEfSe) demonstrated that potential pathogens were enriched in the polluted cloud samples, whereas the diverse ecological function groups were significant in the non-polluted samples. Discrepant community structure determined by redundancy analysis (RDA) indicated that the major ions in cloud water and PM2. 5 in the atmosphere have a negative impact on bacteria, playing a vital role in shaping microbial community structure. The major ions might provide nutrition to bacteria and directly influence the bacterial community, whereas PM2. 5 in air has an indirect impact on bacterial community structure. During wet deposition, soluble particulate matter was dissolved in water droplets resulting in elevated concentration in cloud water. PM2. 5 was possibly associated with different origins and pathways of air mass as determined using source tracking by the backward trajectory, mainly related to long-range transport. This work enhanced our understanding of the characteristics of bacterial ecology in the atmospheric aqueous phase, highlighting the potential influence of environmental variables on the bacterial community in cloud processes. It may provide fundamental information of the bacterial community response in cloud water under increasing pollution. However, due to the limited sample size (13 samples) collected at the summit of Mt Tai, these issues need in-depth discussion. Further studies based on an annual series of field observation experiments and laboratory simulations will continue to track these issues.

scholarly journals Characteristics of bacterial community in fog water at Mt. Tai: similarity and disparity under polluted and non-polluted fog episodes

2016 ◽  
Author(s):  
Min Wei ◽  
Caihong Xu ◽  
Jianmin Chen ◽  
Chao Zhu ◽  
Jiarong Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Environmental Influence ◽  
Community Response ◽  
Ecological Function ◽  
Rrna Gene ◽  
Significant Group ◽  
Structure Variation ◽  
Fog Water ◽  
Wide Range

Abstract. Bacteria, widely distributed in atmospheric bioaerosols, are indispensable component in fog water system and play an important role in atmospheric hydrological cycle. However, little is known about the bacterial community dynamics and ecological function, especially under the increasing serious air pollution events in North China Plain. Here we have a comprehensive characterization of bacterial community structure, variation and environmental influence about fog water collected at Mt. Tai under polluted and non-polluted fog episodes from 24 Jul to 23 Aug 2014. Using the Miseq 16S rRNA gene sequencing, the facts that fog water harbored a highly diverse bacterial community and the predominant phyla of Proteobacteria, Bacteroidetes, Cyanobacteria and Firmicutes were investigated. The abundant genera Acinetobacter, Stenotrophomonas, Pseudomonas, and Empedobacter originated from a wide range of habitat included opportunistic pathogenic and functional species, suggesting the bacterial ecological and healthy importance in fog water should be concerned. Clustering analysis including hierarchical cluster (Hcluster) and principal coordinate analysis (PCoA) indicated a significant disparity between polluted and non-polluted samples. Potential pathogens were significant group in the polluted samples, whereas a more diverse ecological function group of bacteria were identified in the non-polluted samples using linear discriminant analysis effect size (LefSe). Community structure discrepant performed by redundancy analysis (RDA) indicated PM2.5 have negative impact on bacteria, playing vital role in shaping microbial community structure. PM2.5 was possibly associated with different origins and pathways of air mass using source tracking by the backward trajectory and wind analysis, mainly related to the long-term transport combing with local regional emission processes. This work furthered our understanding of bacterial ecological characteristics in the atmospheric aqueous phase, highlighted the potential influence of environmental variables on bacterial community over fog process, which will provide fundamental acquaintance of bacterial community response in fog water under increasing pollution stress.

scholarly journals Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qian Wang ◽  
Xuelan Chen ◽  
Huan Hu ◽  
Xiaoyuan Wei ◽  
Xiaofan Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Structural Changes ◽  
Dental Fluorosis ◽  
Bacterial Species ◽  
Fusobacterium Nucleatum ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Diseases

AbstractDental fluorosis is a very prevalent endemic disease. Although oral microbiome has been reported to correlate with different oral diseases, there appears to be an absence of research recognizing any relationship between the severity of dental fluorosis and the oral microbiome. To this end, we investigated the changes in oral microbial community structure and identified bacterial species associated with moderate and severe dental fluorosis. Salivary samples of 42 individuals, assigned into Healthy (N = 9), Mild (N = 14) and Moderate/Severe (M&S, N = 19), were investigated using the V4 region of 16S rRNA gene. The oral microbial community structure based on Bray Curtis and Weighted Unifrac were significantly changed in the M&S group compared with both of Healthy and Mild. As the predominant phyla, Firmicutes and Bacteroidetes showed variation in the relative abundance among groups. The Firmicutes/Bacteroidetes (F/B) ratio was significantly higher in the M&S group. LEfSe analysis was used to identify differentially represented taxa at the species level. Several genera such as Streptococcus mitis, Gemella parahaemolysans, Lactococcus lactis, and Fusobacterium nucleatum, were significantly more abundant in patients with moderate/severe dental fluorosis, while Prevotella melaninogenica and Schaalia odontolytica were enriched in the Healthy group. In conclusion, our study indicates oral microbiome shift in patients with moderate/severe dental fluorosis. We identified several differentially represented bacterial species enriched in moderate and severe fluorosis. Findings from this study suggests that the roles of these bacteria in oral health and related diseases warrant more consideration in patients with moderate and severe fluorosis.

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