scholarly journals Skin microbiota differs drastically between co-occurring frogs and newts

2017 ◽  
Vol 4 (4) ◽  
pp. 170107 ◽  
Author(s):  
Molly C. Bletz ◽  
R. G. Bina Perl ◽  
Miguel Vences
Keyword(s):  
Bacterial Communities ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Amphibian Skin ◽  
Skin Microbiota ◽  
Triturus Cristatus ◽  
Bacterial Composition ◽  
Host Ecology ◽  
Rana Dalmatina ◽  
Ichthyosaura Alpestris

Diverse microbial assemblages inhabit amphibian skin and are known to differ among species; however, few studies have analysed these differences in systems that minimize confounding factors, such as season, location or host ecology. We used high-throughput amplicon sequencing to compare cutaneous microbiotas among two ranid frogs ( Rana dalmatina, R. temporaria ) and four salamandrid newts ( Ichthyosaura alpestris, Lissotriton helveticus, L. vulgaris, Triturus cristatus ) breeding simultaneously in two ponds near Braunschweig, Germany. We found that bacterial communities differed strongly and consistently between these two distinct amphibian clades. While frogs and newts had similar cutaneous bacterial richness, their bacterial composition strongly differed. Average Jaccard distances between frogs and newts were over 0.5, while between species within these groups distances were only 0.387 and 0.407 for frogs and newts, respectively. At the operational taxonomic unit (OTU) level, 31 taxa exhibited significantly different relative abundances between frogs and newts. This finding suggests that chemical or physical characteristics of these amphibians' mucosal environments provide highly selective conditions for bacterial colonizers. Multi-omics analyses of hosts and their microbiota as well as directed efforts to understand chemical differences in the mucosal environments (e.g. pH), and the specificities of host-produced compounds against potential colonizers will help to better understand this intriguing pattern.

scholarly journals Profiling the Bacterial Diversity in a Typical Karst Tiankeng of China

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 187 ◽  
Author(s):  
Gaozhong Pu ◽  
Yanna Lv ◽  
Lina Dong ◽  
Longwu Zhou ◽  
Kechao Huang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Operational Taxonomic Unit ◽  
Soil Characteristics ◽  
Soil Samples ◽  
Controlling Factors ◽  
Bacterial Composition ◽  
Microbial Distribution ◽  
Significant Difference

While karst tiankengs have a higher capacity to act as safe havens for biodiversity in changing climates, little is known about their soil microorganisms. To fill this gap, we investigate the distribution and driving factors of the bacterial community in karst tiankeng systems. There is a significant difference in the soil characteristics between the inside and the outside of a karst tiankeng. At the karst tiankeng considered in this study, the bacterial composition, in terms of the operational taxonomic unit (OTU), was found to be significantly different in different soil samples, taken from diverse sampling sites within the collapsed doline or the external area, and showed a high habitat heterogeneity. The dominant phylum abundances vary with the sampling sites and have their own indicator taxa from phylum to genus. Unlike the primary controlling factors of plant diversity, the microclimate (soil moisture and temperature), soil pH, and slope dominated the distribution of the bacterial community in karst tiankeng systems. Our results firstly showed the distribution characteristics of bacterial communities and then revealed the importance of microhabitats in predicting the microbial distribution in karst tiankeng systems.

scholarly journals Early changes in bacterial communities in wound tissues of Pinus massoniana after inoculation with Bursaphelenchus xylophilus

Nematology ◽  
2020 ◽  
Vol 23 (1) ◽  
pp. 89-101
Author(s):  
Jinyan Liu ◽  
Songqing Wu ◽  
Xia Hu ◽  
Wanfeng Xie ◽  
Xiuping Huang ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Pinus Massoniana ◽  
Amplicon Sequencing ◽  
Bursaphelenchus Xylophilus ◽  
Bacterial Composition ◽  
Invasion Mechanism ◽  
16S Rdna Amplicon Sequencing ◽  
Abundant Genus ◽  
Functional Analyses ◽  
Shed Light

Summary The bacterial communities in the wound tissues of Pinus massoniana were analysed by 16S rDNA amplicon sequencing. The results showed that the bacterial richness and diversity changed remarkably whether the wound was inoculated with pine wood nematode (PWN; Bursaphelenchus xylophilus) or not after 12 h. However, the predominant bacteria Stenotrophomonas, Burkholderiaceae, Pseudomonas, Serratia and Delftia, introduced by PWN in the wound tissues, changed within 6 h. After 6 h of PWN inoculation, the most abundant genus associating with PWN, Stenotrophomonas, failed to colonise the wound tissues, and the abundance of Delftia decreased, while the other representative bacteria, Burkholderiaceae, Pseudomonas and Serratia, from the PWN were markedly enriched. In addition, our study is the first to report the association of Serratia liquefaciens with PWN. Predicted functional analyses using the Tax4Fun tool showed that the alterations in bacterial composition also led to shifts in their functional pathways, especially after 12 h of PWN inoculation. These findings clarified that the bacteria carried by PWN were responsible for the alterations in bacterial communities in the wound tissues and will shed light on the invasion mechanism of PWN.

scholarly journals Analysis of Bacterial Diversity in Relation to the Presence of the Top 7 Shiga Toxin–Producing Escherichia coli throughout Australian Beef Abattoirs

2020 ◽  
Vol 83 (10) ◽  
pp. 1812-1821
Author(s):  
SANGA KANG ◽  
JOSHUA T. RAVENSDALE ◽  
RANIL COOREY ◽  
GARY A. DYKES ◽  
ROBERT S. BARLOW
Keyword(s):  
Escherichia Coli ◽  
Bacterial Diversity ◽  
Shiga Toxin ◽  
Bacterial Communities ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Bacterial Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Surface Samples ◽  
Inspection Service

ABSTRACT There is increasing evidence that diversity changes in bacterial communities of beef cattle correlate to the presence of Shiga toxin–producing Escherichia coli (STEC). However, studies that found an association between STEC and bacterial diversity have been focused on preslaughter stages in the beef supply chain. This study was designed to test a hypothesis that there are no differences in bacterial diversity between samples with and those without the presence of the top 7 STEC (O26, O45, O103, O111, O121, O145, and O157) throughout processing in an integrated (abattoir A) and a fragmented (abattoir B) Australian beef abattoir. Slaughter and boning room surface samples from each abattoir were analyzed using 16S rRNA amplicon sequencing and tested for the top 7 STEC following the Food Safety and Inspection Service protocol. Potential positives through slaughter were similar between the abattoirs (64 to 81%). However, abattoir B had substantially reduced potential positives in the boning room compared with abattoir A (abattoir A: 23 and 48%; abattoir B: 2 and 7%). Alpha diversity between the sample groups was not significantly different (P > 0.05) regardless of different STEC markers. Nonmetric multidimensional scaling of slaughter samples showed that the bacterial composition in fecal and hide samples shared the least similarity with the communities in carcass and environmental samples. Surface samples from slaughter (carcass and environmental) and boning (carcass, beef trim, and environmental) all appeared randomly plotted on the scale. This indicated that the STEC presence also did not have a significant effect (P > 0.05) on beta diversity. Although presence of STEC appeared to correlate with changes in diversity of fecal and hide bacterial communities in previous studies, it did not appear to have the same effect on other samples throughout processing. HIGHLIGHTS

scholarly journals Bacterial Diversity in Soil Surround Subterranean Termites-Damaged Wooden Buildings in Seonamsa Temple and Effect of the Termites on Bacterial Diversity in Humus Soil

2021 ◽  
Vol 37 (4) ◽  
pp. 357-361
Author(s):  
Young Hee Kim ◽  
Boa Lim ◽  
Jeung Min Lee ◽  
Jin Young Hong ◽  
Soo Ji Kim ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Operational Taxonomic Unit ◽  
Illumina Miseq ◽  
Subterranean Termites ◽  
Bacterial Composition ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Humus Soil

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple’s soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple’s soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

scholarly journals Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alexander Munoz ◽  
Matthew R. Hayward ◽  
Seth M. Bloom ◽  
Muntsa Rocafort ◽  
Sinaye Ngcapu ◽  
...  
Keyword(s):  
High Risk ◽  
Bacterial Communities ◽  
High Probability ◽  
Temporal Dynamics ◽  
Transition Probabilities ◽  
Low Risk ◽  
Sub Saharan Africa ◽  
Reproductive Outcomes ◽  
Bacterial Composition ◽  
Sub Saharan

Abstract Background Cervicovaginal bacterial communities composed of diverse anaerobes with low Lactobacillus abundance are associated with poor reproductive outcomes such as preterm birth, infertility, cervicitis, and risk of sexually transmitted infections (STIs), including human immunodeficiency virus (HIV). Women in sub-Saharan Africa have a higher prevalence of these high-risk bacterial communities when compared to Western populations. However, the transition of cervicovaginal communities between high- and low-risk community states over time is not well described in African populations. Results We profiled the bacterial composition of 316 cervicovaginal swabs collected at 3-month intervals from 88 healthy young Black South African women with a median follow-up of 9 months per participant and developed a Markov-based model of transition dynamics that accurately predicted bacterial composition within a broader cross-sectional cohort. We found that Lactobacillus iners-dominant, but not Lactobacillus crispatus-dominant, communities have a high probability of transitioning to high-risk states. Simulating clinical interventions by manipulating the underlying transition probabilities, our model predicts that the population prevalence of low-risk microbial communities could most effectively be increased by manipulating the movement between L. iners- and L. crispatus-dominant communities. Conclusions The Markov model we present here indicates that L. iners-dominant communities have a high probability of transitioning to higher-risk states. We additionally identify transitions to target to increase the prevalence of L. crispatus-dominant communities. These findings may help guide future intervention strategies targeted at reducing bacteria-associated adverse reproductive outcomes among women living in sub-Saharan Africa.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals 18S rRNA Analysis Reveals High Diversity of Phytoplankton with Emphasis on a Naked Dinoflagellate Gymnodinium sp. at the Han River (Korea)

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 73
Author(s):  
Buhari Lawan Muhammad ◽  
Taehee Kim ◽  
Jang-Seu Ki
Keyword(s):  
Water Quality ◽  
Quality Management ◽  
18S Rrna ◽  
Water Quality Management ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Freshwater Ecosystems ◽  
Reservoir Area ◽  
Han River ◽  
Phytoplankton Communities

Biomonitoring of phytoplankton communities in freshwater ecosystems is imperative for efficient water quality management. In the present study, we present the seasonal diversity of phytoplankton from the non-reservoir area of the Han River (Korea), assessed using the 18S rRNA amplicon sequencing. Our results uncovered a considerably high eukaryotic diversity, which was predominantly represented by phytoplankton in all the seasons (38–63%). Of these, the diatoms, Cyclostephanos tholiformis, Stephanodiscus hantzschii, and Stephanodiscus sp., were frequently detected in spring and winter. Interestingly, for the first time in the Han River, we detected a large number of operational taxonomic unit (OTU) reads belonging to the naked dinoflagellate Gymnodinium sp., which dominated in autumn (15.8%) and was observed only in that season. Molecular cloning and quantitative real-time polymerase chain reaction (PCR) confirmed the presence of Gymnodinium sp. in the samples collected in 2012 and 2019. Moreover, a comparison of the present data with our previous data from a reservoir area (Paldang Dam) revealed similar patterns of phytoplankton communities. This molecular approach revealed a prospective toxic species that was not detected through microscopy. Collectively, resolving phytoplankton communities at a level relevant for water quality management will provide a valuable reference for future studies on phytoplankton for environmental monitoring.

scholarly journals From the Andes to the desert: First overview of the bacterial community in the Rimac river, the main source of water for Lima, Peru

2020 ◽  
Author(s):  
Pedro E. Romero ◽  
Erika Calla-Quispe ◽  
Camila Castillo-Vilcahuaman ◽  
Mateo Yokoo ◽  
Hammerly Lino Fuentes-Rivera ◽  
...  
Keyword(s):  
Metropolitan Area ◽  
Bacterial Communities ◽  
Geographical Location ◽  
Microbiological Quality ◽  
Amplicon Sequencing ◽  
Urban Sewage ◽  
16S Rrna Amplicon Sequencing ◽  
The Andes ◽  
Metabolic Functions ◽  
Quality Assessments

AbstractBackgroundThe Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. We aim to produce the first characterization of bacterial communities in the Rimac river using a 16S rRNA amplicon sequencing approach which would be useful to identify bacterial diversity and potential understudied pathogens.ResultsWe report a higher diversity in bacterial communities from the Upper and, especially, Middle Rimac compared to the Lower Rimac (Metropolitan zone). Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility, quorum sensing and xenobiotics metabolism. Additional metabolomic analyses showed the presence natural flavonoids and antibiotics in the Upper Rimac, and herbicides in the Lower Rimac.ConclusionsThe dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, but that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

Community dynamics of duckweed-associated bacteria upon inoculation of plant growth-promoting bacteria

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Hidehiro Ishizawa ◽  
Masashi Kuroda ◽  
Daisuke Inoue ◽  
Masaaki Morikawa ◽  
Michihiko Ike
Keyword(s):  
Plant Growth ◽  
Bacterial Communities ◽  
Production Efficiency ◽  
Community Dynamics ◽  
Amplicon Sequencing ◽  
Plant Colonization ◽  
Plant Growth Promoting Bacteria ◽  
Short Period ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT Plant growth-promoting bacteria (PGPB) have recently been demonstrated as a promising agent to improve wastewater treatment and biomass production efficiency of duckweed hydrocultures. With a view to their reliable use in aqueous environments, this study analysed the plant colonization dynamics of PGPB and the ecological consequences for the entire duckweed-associated bacterial community. A PGPB strain, Aquitalea magnusonii H3, was inoculated to duckweed at different cell densities or timings in the presence of three environmental bacterial communities. The results showed that strain H3 improved duckweed growth by 11.7–32.1% in five out of nine experiments. Quantitative-PCR and amplicon sequencing analyses showed that strain H3 successfully colonized duckweed after 1 and 3 d of inoculation in all cultivation tests. However, it significantly decreased in number after 7 d, and similar bacterial communities were observed on duckweed regardless of H3 inoculation. Predicted metagenome analysis suggested that genes related to bacterial chemotactic motility and surface attachment systems are consistently enriched through community assembly on duckweed. Taken together, strain H3 dominantly colonized duckweed for a short period and improved duckweed growth. However, the inoculation of the PGPB did not have a lasting impact due to the strong resilience of the natural duckweed microbiome.

scholarly journals The Skin Microbiota of Eleutherodactylus Frogs: Effects of Host Ecology, Phylogeny, and Local Environment

2019 ◽  
Vol 10 ◽  
Author(s):  
Liza Garcia-Recinos ◽  
Patricia A. Burrowes ◽  
Maria Dominguez-Bello
Keyword(s):  
Local Environment ◽  
Skin Microbiota ◽  
Host Ecology
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