Iron Bacterial Phylogeny and their Execution Towards Iron Availability in Equatorial Indian Ocean and Coastal Arabian Sea

Based on distinct colony morphology, color, size, shape and certain other traits, 92 bacterial isolates were investigated to understand their managerial ability on iron from the Arabian Sea and Equatorial Indian Ocean samples. The ARDRA (amplified rDNA restriction analysis) applied to eliminate the duplication of the bacterial strains, resulted 39 different banding patterns. The 16S rRNA gene sequencing data indicate the dominancy of three phylogenetic groups, alpha-Proteobacteria (10.25%), gamma-Proteobacteria (35.89%) and Bacilli (53.84%) in these waters. Marinobacter and Bacillus were the only common genera from both of the regions. Pseudoalteromonas, Halomonas, Rheinheimera, Staphylococcus and Idiomarina were some of the other genera obtained from the Arabian Sea. Erythrobacter, Roseovarius, Sagittula and Nitratireductor were found mostly in Equatorial Indian Ocean. In addition, 16S rRNA gene sequence data of some of our iron bacterial strains belong to novel species and one isolate ASS2A could form a new genus. Close to 23% of the isolates were able to produce high affinity sets of ligands like siderophores to mediate iron transport into the cell. The current study indicated that the Equatorial Indian Ocean species were well adapted to oxidize iron as an electron acceptor and the Arabian Sea species preferably go through siderophore production.

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16S rRNA Gene Amplicon Sequencing Data of Tailing and Nontailing Rhizosphere Soils of Mimosa pudica from a Heavy Metal-Contaminated Ex-Tin Mining Area

Microbiology Resource Announcements ◽

10.1128/mra.00761-20 ◽

2020 ◽

Vol 9 (42) ◽

Author(s):

Saidu Abdullahi ◽

Hazzeman Haris ◽

Kamarul Z. Zarkasi ◽

Hamzah G. Amir

Keyword(s):

Heavy Metal ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Mimosa Pudica ◽

Sequencing Data ◽

Content Type ◽

Rhizosphere Soils

ABSTRACT The 16S rRNA gene amplicon sequence data from tailing and nontailing rhizosphere soils of Mimosa pudica from a heavy metal-contaminated area are reported here. Diverse bacterial taxa were represented in the results, and the most dominant phyla were Proteobacteria (41.2%), Acidobacteria (17.1%), and Actinobacteria (14.4%).

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Analysis of the bacterial community within carrot wash water

Canadian Journal of Microbiology ◽

10.1139/w11-013 ◽

2011 ◽

Vol 57 (5) ◽

pp. 447-452 ◽

Cited By ~ 13

Author(s):

Lena Hausdorf ◽

Antje Fröhling ◽

Oliver Schlüter ◽

Michael Klocke

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Restriction Analysis ◽

Meat Products ◽

Nucleotide Sequences ◽

Wash Water ◽

Rrna Gene ◽

Inorganic Particles ◽

Amplified Rdna Restriction Analysis

Vegetables are washed after harvest to remove unwanted organic and inorganic particles, but wash water contaminated with certain pathogenic microorganisms can potentially contaminate produce. In this study, the microbial diversity of wash water was analyzed in samples taken from a carrot-processing facility. A 16S rRNA gene library with 427 clones was constructed and analyzed by amplified rDNA restriction analysis. For taxonomic classification, the 16S rRNA gene nucleotide sequences of 94 amplified rDNA restriction analysis fingerprints were determined. Each fingerprint indicates a distinct group of microorganisms. The nucleotide sequences were assigned to corresponding reference species. The most prevalent genus was Tolumonas , with 26% of the clones, followed by Acinetobacter and Flacobacterium , with 11% each. The latter two genera contain species that are known to cause nosocomial infections. The fourth most common genus was Arcobacter , comprising 9% of all clones. Some species of Arcobacter are considered to be emerging food pathogens, mainly associated with the contamination of meat products. So far, they have not been considered as contaminants of fresh produce. Based on the sequence data, an Arcobacter-specific PCR assay was developed to facilitate the detection of vegetable-associated Arcobacter strains.

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Microbacterium indicum sp. nov., isolated from a deep-sea sediment sample from the Chagos Trench, Indian Ocean

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64782-0 ◽

2007 ◽

Vol 57 (8) ◽

pp. 1819-1822 ◽

Cited By ~ 33

Author(s):

S. Shivaji ◽

Bhaskar Bhadra ◽

R. Sreenivas Rao ◽

Preeti Chaturvedi ◽

Pavan Kumar Pindi ◽

...

Keyword(s):

Indian Ocean ◽

16S Rrna ◽

16S Rrna Gene ◽

Deep Sea ◽

Sediment Sample ◽

Sequence Similarity ◽

Rrna Gene ◽

Bacterial Strains ◽

Phenotypic Characteristics ◽

Deep Sea Sediment

Two bacterial strains, BBH6T and BBH9, were isolated from a deep-sea sediment sample collected from the Chagos Trench, Indian Ocean, at a depth of 5904 m. The two strains were closely related in their 16S rRNA gene sequences (99.7 %), belonged to one genomic species and were virtually identical at the phenotypic level. Microbacterium barkeri DSM 20145T was the nearest phylogenetic neighbour to the new isolates, with 16S rRNA gene sequence similarity levels of 97.2–97.4 %. The new isolates exhibited levels of DNA–DNA relatedness of 32–34 % to M. barkeri and differed from it in a number of phenotypic characteristics. Therefore, it is suggested that strains BBH6T and BBH9 represent a novel species of the genus Microbacterium, for which the name Microbacterium indicum sp. nov. is proposed. The type strain is BBH6T (=LMG 23459T=IAM 15355T).

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Microbiome of Odontogenic Abscesses

Microorganisms ◽

10.3390/microorganisms9061307 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1307

Author(s):

Sebastian Böttger ◽

Silke Zechel-Gran ◽

Daniel Schmermund ◽

Philipp Streckbein ◽

Jan-Falco Wilbrand ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Oral Microbiome ◽

Minor Role ◽

Rrna Gene ◽

Sequencing Analysis ◽

Bacterial Strains ◽

16S Rrna Gene Analysis ◽

Odontogenic Infections ◽

Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.01541-09 ◽

2009 ◽

Vol 75 (23) ◽

pp. 7537-7541 ◽

Cited By ~ 11597

Author(s):

Patrick D. Schloss ◽

Sarah L. Westcott ◽

Thomas Ryabin ◽

Justine R. Hall ◽

Martin Hartmann ◽

...

Keyword(s):

16S Rrna ◽

Software Package ◽

Sequence Data ◽

Rrna Gene ◽

Sequencing Data ◽

Laptop Computer ◽

Operational Taxonomic Units ◽

Β Diversity ◽

Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

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Epipelic cyanobacterial diversity in Pinang River basin, Malaysia, revealed by 16S-based metagenomic approach

Algologia ◽

10.15407/alg31.01.093 ◽

2021 ◽

Vol 31 (1) ◽

pp. 93-113

Author(s):

A.R. Nur Fadzliana ◽

◽

W.O. Wan Maznah ◽

S.A.M. Nor ◽

Choon Pin Foong ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

River Basin ◽

Sequence Data ◽

Diversity Index ◽

Saline Water ◽

Illumina Miseq ◽

Rrna Gene ◽

Cyanobacterial Community ◽

Upstream Station

Cyanobacteria are the most widespread group of photosynthetic prokaryotes. They are primary producers in a wide variety of habitats and are able to thrive in harsh environments, including polluted waters; therefore, this study was conducted to explore the cyanobacterial populations inhabiting river tributaries with different levels of pollution. Sediment samples (epipelon) were collected from selected tributaries of the Pinang River basin. Air Terjun (T1) and Air Itam rivers (T2) represent the upper streams of Pinang River basin, while Dondang (T3) and Jelutong rivers (T4) are located at in the middle of the river basin. The Pinang River (T5) is located near the estuary and is subjected to saline water intrusion during high tides. Cyanobacterial community was determined by identifying the taxa via 16S rRNA gene amplicon sequence data. 16S rRNA gene amplicons generated from collected samples were sequenced using illumina Miseq, with the targeted V3 and V4 regions yielding approximately 1 mln reads per sample. Synechococcus, Phormidium, Arthronema and Leptolyngbya were found in all samples. Shannon-Weiner diversity index was highest (H’ = 1.867) at the clean upstream station (T1), while the moderately polluted stream (T3) recorded the lowest diversity (H’ = 0.399), and relatively polluted stations (T4 and T5) recorded fairly high values of H’. This study provides insights into the cyanobacterial community structure in Pinang River basin via cultivation-independent techniques using 16S rRNA gene amplicon sequence. Occurrence of some morphospecies at specific locations showed that the cyanobacterial communities are quite distinct and have specific ecological demands. Some species which were ubiquitous might be able to tolerate varied environmental conditions.

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Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

Frontiers in Microbiology ◽

10.3389/fmicb.2021.742000 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marc Crampon ◽

Coralie Soulier ◽

Pauline Sidoli ◽

Jennifer Hellal ◽

Catherine Joulian ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Soil Microbial Communities ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Treated Wastewater ◽

Rrna Gene ◽

Sequencing Data ◽

Rrna Gene Sequencing

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

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Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.069864-0 ◽

2015 ◽

Vol 65 (Pt_2) ◽

pp. 723-731 ◽

Cited By ~ 38

Author(s):

Ronel Roberts ◽

Emma T. Steenkamp ◽

Gerhard Pietersen

Keyword(s):

South Africa ◽

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Nucleotide Sequence Data ◽

Trioza Erytreae

Greening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.

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Jinshanibacter allomyrinae sp. nov., isolated from larvae of Allomyrina dichotoma, proposal of Insectihabitans xujianqingii gen. nov., comb. nov. and emended descriptions of the genera Jinshanibacter, Limnobaculum and Pragia

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004938 ◽

2021 ◽

Vol 71 (8) ◽

Author(s):

Soon Dong Lee ◽

Yeong-Sik Byeon ◽

Sung-Min Kim ◽

Hong Lim Yang ◽

In Seop Kim

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Sequence Similarity ◽

Rrna Gene ◽

Bacterial Strains ◽

Content Type ◽

Gene Phylogeny ◽

Link Type ◽

Protaetia Brevitarsis Seulensis

Taxonomic positions of four Gram-negative bacterial strains, which were isolated from larvae of two insects in Jeju, Republic of Korea, were determined by a polyphasic approach. Strains CWB-B4, CWB-B41 and CWB-B43 were recovered from larvae of Protaetia brevitarsis seulensis, whereas strain BWR-B9T was from larvae of Allomyrina dichotoma. All the isolates grew at 10–37 °C, at pH 5.0–9.0 and in the presence of 4 % (w/v) NaCl. The 16S rRNA gene phylogeny showed that the four isolates formed two distinct sublines within the order Enterobacteriales and closely associated with members of the genus Jinshanibacter . The first group represented by strain CWB-B4 formed a tight cluster with Jinshanibacter xujianqingii CF-1111T (99.3 % sequence similarity), whereas strain BWR-B9T was most closely related to Jinshanibacter zhutongyuii CF-458T (99.5 % sequence similarity). The 92 core gene analysis showed that the isolates belonged to the family Budviciaceae and supported the clustering shown in 16S rRNA gene phylogeny. The genomic DNA G+C content of the isolates was 45.2 mol%. A combination of overall genomic relatedness and phenotypic distinctness supported that three isolates from Protaetia brevitarsis seulensis are different strains of Jinshanibacter xujianqingii , whereas one isolate from Allomyrina dichotoma represents a new species of the genus Jinshanibacter . On the basis of results obtained here, Jinshanibacter allomyrinae sp. nov. (type strain BWR-B9T=KACC 22153T=NBRC 114879T) and Insectihabitans xujianqingii gen. nov., comb. nov. are proposed, with the emended descriptions of the genera Jinshanibacter , Limnobaculum and Pragia .

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Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure

mBio ◽

10.1128/mbio.01454-19 ◽

2019 ◽

Vol 10 (4) ◽

Cited By ~ 5

Author(s):

Marc A. Sze ◽

Begüm D. Topçuoğlu ◽

Nicholas A. Lesniak ◽

Mack T. Ruffin ◽

Patrick D. Schloss

Keyword(s):

Colorectal Cancer ◽

Fatty Acids ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Short Chain Fatty Acids ◽

Tumor Burden ◽

Short Chain ◽

Rrna Gene ◽

Chain Fatty Acids

ABSTRACT Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria that produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with healthy colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power. IMPORTANCE Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals with different colonic tumor burdens who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.

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