Genomic composition of microbiol gingival sulcus and periodontal pockets in young persons

2020 ◽  
Vol 20 (1) ◽  
pp. 19-25
Author(s):  
S. L. S.L. Blashkova ◽  
T. N. Modina ◽  
A. K. Abdrakhmanov ◽  
D. A. Zinecker ◽  
E. V. Mamaeva ◽  
...  
Keyword(s):  
Risk Factors ◽  
Young People ◽  
16S Rrna ◽  
Periodontal Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Periodontal Pocket ◽  
Control Group ◽  
The Republic

Relevance. Risk factors of local importance plays a crucial role in the development of inflammatory periodontal diseases, but the profile of representation and the role of origin microbial markers continues to be refined, what explains the increasing interest by the metagenomic studies. Purpose. To compare the genomic composition of the microbiota of the periodontal sulcus and periodontal pocket by healthy patients with inflammatory periodontal diseases living on the territory of Kazan, the Republic of Tatarstan. Materials and methods. The study included 25 young people (11 boys, 14 girls) aged 18-19 years, with inflammatory periodontal diseases (chronic generalized catarrhal gingivitis (12 people), chronic generalized periodontitis of mild severity (13 people)). The control group consisted of 11 donors without inflammatory periodontal disease.Results. In the present study structures of microbial communities of periodontal spaces has been analyzed with using the sequencing of fragments of bacterial 16s rRNA genes (regions V3 and V4). Results of the analysis allowed to get a real idea of its composition and to determine both known and previously undefined uncultivated phylotypes. Conclusions. It was shown that in the group of the patients with inflammatory periodontal diseases there were identified 183 phylotypes at the level of genus (Mogibacteriacea, TM7 3, Rs–045, Dethiosulfovibrionaceae) relating to 17 phyls (phylum), that is a synonym of type in taxonomy (taxon between Kingdom and class). By the patients with chronic generalized periodontitis of mild severity, it was not possible to reliably isolate the phylotypes present in increased amounts in relation to chronic catarrhal gingivitis; in relation to control – there was a statistically significant increase in the proportion of families Porphyromonadaceae, Peptostreptococcaceae and the proportion of genera Dialister, Filifactor, Parvimonas, Tannerella, Treponema. 

scholarly journals Coaggregation among Nonflocculating Bacteria Isolated from Activated Sludge

2003 ◽  
Vol 69 (10) ◽  
pp. 6056-6063 ◽  
Author(s):  
Anushree Malik ◽  
Masashi Sakamoto ◽  
Shohei Hanazaki ◽  
Masamitsu Osawa ◽  
Takanori Suzuki ◽  
...  
Keyword(s):  
16S Rrna ◽  
Activated Sludge ◽  
Aggregate Size ◽  
Spectrophotometric Assay ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Acinetobacter Junii ◽  
Acinetobacter Johnsonii

ABSTRACT Thirty-two strains of nonflocculating bacteria isolated from sewage-activated sludge were tested by a spectrophotometric assay for their ability to coaggregate with one other in two-membered systems. Among these strains, eight showed significant (74 to 99%) coaggregation with Acinetobacter johnsonii S35 while only four strains coaggregated, to a lesser extent (43 to 65%), with Acinetobacter junii S33. The extent and pattern of coaggregation as well as the aggregate size showed good correlation with cellular characteristics of the coaggregating partners. These strains were identified by sequencing of full-length 16S rRNA genes. A. johnsonii S35 could coaggregate with strains of several genera, such as Oligotropha carboxidovorans, Microbacterium esteraromaticum, and Xanthomonas spp. The role of Acinetobacter isolates as bridging organisms in multigeneric coaggregates is indicated. This investigation revealed the role of much-neglected nonflocculating bacteria in floc formation in activated sludge.

scholarly journals Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

mBio ◽  
2013 ◽  
Vol 4 (3) ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Daniel Lundin ◽  
Matthias Labrenz ◽  
Klaus Jürgens ◽  
Zongli Zheng ◽  
...  
Keyword(s):  
16S Rrna ◽  
Carbon Cycle ◽  
Baltic Sea ◽  
Glycoside Hydrolases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sulfated Polysaccharides ◽  
The Baltic Sea ◽  
The Baltic

ABSTRACTThe verrucomicrobial subdivision 2 classSpartobacteriais one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of theSpartobacteriais one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within theSpartobacteriaexists. Since no aquatic representative from theSpartobacteriahas been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic SeaSpartobacteriaphylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype’s distribution within the Baltic Sea indicate a connection toCyanobacteriathat may be the main source of the polysaccharide substrates.IMPORTANCEThe ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the classSpartobacteriawithin theVerrucomicrobiathat, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquaticVerrucomicrobiaby applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able toin silicoisolate genome fragments belonging to a phylotype of theSpartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs withCyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.

scholarly journals Natural Niche for Organohalide-Respiring Chloroflexi

2011 ◽  
Vol 78 (2) ◽  
pp. 393-401 ◽  
Author(s):  
Mark J. Krzmarzick ◽  
Benjamin B. Crary ◽  
Jevon J. Harding ◽  
Oyenike O. Oyerinde ◽  
Alessandra C. Leri ◽  
...  
Keyword(s):  
16S Rrna ◽  
Terrestrial Ecosystems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Core ◽  
Content Type ◽  
Integral Role ◽  
Terrestrial Environments ◽  
Inorganic Chloride

ABSTRACTThe phylumChloroflexicontains several isolated bacteria that have been found to respire a diverse array of halogenated anthropogenic chemicals. The distribution and role of theseChloroflexiin uncontaminated terrestrial environments, where abundant natural organohalogens could function as potential electron acceptors, have not been studied. Soil samples (116 total, including 6 sectioned cores) from a range of uncontaminated sites were analyzed for the number ofDehalococcoides-likeChloroflexi16S rRNA genes present.Dehalococcoides-likeChloroflexipopulations were detected in all but 13 samples. The concentrations of organochlorine ([organochlorine]), inorganic chloride, and total organic carbon (TOC) were obtained for 67 soil core sections. The number ofDehalococcoides-likeChloroflexi16S rRNA genes positively correlated with [organochlorine]/TOC while the number ofBacteria16S rRNA genes did not.Dehalococcoides-likeChloroflexiwere also observed to increase in number with a concomitant accumulation of chloride when cultured with an enzymatically produced mixture of organochlorines. This research provides evidence that organohalide-respiringChloroflexiare widely distributed as part of uncontaminated terrestrial ecosystems, they are correlated with the fraction of TOC present as organochlorines, and they increase in abundance while dechlorinating organochlorines. These findings suggest that organohalide-respiringChlorofleximay play an integral role in the biogeochemical chlorine cycle.

scholarly journals Characteristics of gut microbiota in people with obesity

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255446
Author(s):  
Mengmeng Duan ◽  
Yuezhu Wang ◽  
Qiang Zhang ◽  
Rong Zou ◽  
Min Guo ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Sequencing Data ◽  
Genome Database ◽  
Control Subjects ◽  
And Control

Background Obesity is the cause of cardiovascular diseases and other diseases, leading to increased medical costs, and causing a great burden to individuals, families and society. The prevalence of obesity is increasing and has become a global health problem. There is growing evidence that gut microbiota plays an important role in obesity. In this article, we revealed the differences in the gut microbiota between 21 people with obesity and 21 control subjects, and predicted the functional potential changes by 16S rRNA sequencing of the fecal bacteria of the subjects. Methods The raw sequencing data of 21 healthy Beijing volunteers was downloaded from Microbial Genome Database System. Microbial 16S rRNA genes of 21 adults with obesity were sequenced on an Illumina MiSeq instrument and analyzed by using bioinformatics and statistical methods. Results The diversity of gut microbiota in people with obesity decreased significantly. There were significant differences in gut microbiota between the Obesity and Control group at different levels. At the phylum level, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria are significantly different between the Obesity and Control group. In people with obesity, the ratio of Firmicutes/Bacteroidetes decreased significantly. At the genus level, there were significant differences among the 16 major genera, of which four genera Prevotella, Megamonas, Fusobacterium and Blautia increased significantly in people with obesity, while the remaining 12 genera, Faecalibacterium, Lachnospiracea_incertae_sedis, Gemmiger and Clostridium XlVa, etc. decreased significantly. At the species level, nine species including Bacteroides uniformis and Prevotella copri had significant differences. Compared with the control group, subjects with obesity were abnormalities in 57 pathways, mainly in Carbohydrate metabolism and Lipid metabolism. Conclusions Overall, our study revealed differences in the gut microbiota between people with obesity and control subjects, providing novel target for the treatment of individuals with obesity.

scholarly journals Niche Partitioning of Marine Group I Crenarchaeota in the Euphotic and Upper Mesopelagic Zones of the East China Sea

2011 ◽  
Vol 77 (21) ◽  
pp. 7469-7478 ◽  
Author(s):  
Anyi Hu ◽  
Nianzhi Jiao ◽  
Rui Zhang ◽  
Zao Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Column ◽  
Niche Partitioning ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The East China Sea ◽  
Group I

ABSTRACTMarine group ICrenarchaeota(MGI) represents a ubiquitous and numerically predominant microbial population in marine environments. An understanding of the spatial dynamics of MGI and its controlling mechanisms is essential for an understanding of the role of MGI in energy and element cycling in the ocean. In the present study, we investigated the diversity and abundance of MGI in the East China Sea (ECS) by analysis of crenarchaeal 16S rRNA gene, the ammonia monooxygenase geneamoA, and the biotin carboxylase geneaccA. Quantitative PCR analyses revealed that these genes were higher in abundance in the mesopelagic than in the euphotic zone. In addition, the crenarchaealamoAgene was positively correlated with the copy number of the MGI 16S rRNA gene, suggesting that most of the MGI in the ECS are nitrifiers. Furthermore, the ratios of crenarchaealaccAtoamoAor to MGI 16S rRNA genes increased from the euphotic to the mesopelagic zone, suggesting that the role of MGI in carbon cycling may change from the epipelagic to the mesopelagic zones. Denaturing gradient gel electrophoretic profiling of the 16S rRNA genes revealed depth partitioning in MGI community structures. Clone libraries of the crenarchaealamoAandaccAgenes showed both “shallow” and “deep” groups, and their relative abundances varied in the water column. Ecotype simulation analysis revealed that MGI in the upper ocean could diverge into special ecotypes associated with depth to adapt to the light gradient across the water column. Overall, our results showed niche partitioning of the MGI population and suggested a shift in their ecological functions between the euphotic and mesopelagic zones of the ECS.

scholarly journals Effects of respiratory disease on Kele piglets lung microbiome, assessed through 16S rRNA sequencing

2020 ◽  
Vol 13 (9) ◽  
pp. 1970-1981
Author(s):  
Jing Zhang ◽  
Kaizhi Shi ◽  
Jing Wang ◽  
Xiong Zhang ◽  
Chunping Zhao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Respiratory Tract ◽  
Respiratory System ◽  
Respiratory Diseases ◽  
Lavage Fluid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Control Group ◽  
Composition Analysis ◽  
Α Diversity

Background and Aim: Due to the incomplete development of the immune system in immature piglets, the respiratory tract is susceptible to invasion by numerous pathogens that cause a range of potential respiratory diseases. However, few studies have reported the changes in pig lung microorganisms during respiratory infection. Therefore, we aimed to explore the differences in lung environmental microorganisms between healthy piglets and piglets with respiratory diseases. Materials and Methods: Histopathological changes in lung sections were observed in both diseased and healthy pigs. Changes in the composition and abundance of microbiomes in alveolar lavage fluid from eleven 4-week-old Chinese Kele piglets (three clinically healthy and eight diseased) were studied by IonS5TM XL sequencing of the bacterial 16S rRNA genes. Results: Histopathological sections showed that diseased pigs displayed more lung lesions than healthy pigs. Diseased piglets harbored lower bacterial operational taxonomic units, α-diversity, and bacterial community complexity in comparison to healthy piglets. Taxonomic composition analysis showed that in the diseased piglets, the majority of flora was composed of Ureaplasma, Mycoplasma, and Actinobacillus; while Actinobacillus, Sphingomonas, and Stenotrophomonas were dominant in the control group. The abundance of Ureaplasma was significantly higher in ill piglets (p<0.05), and the phylogenetic tree indicated that Ureaplasma was clustered in Ureaplasma diversum, a conditional pathogen that has the potential to affect the swine respiratory system. Conclusion: The results of this study show that the microbial species and structure of piglets' lungs were changed during respiratory tract infection. The finding of Ureaplasma suggested that besides known pathogens such as Mycoplasma and Actinobacillus, unknown pathogens can exist in the respiratory system of diseased pigs and provide a potential basis for clinical treatment.

scholarly journals Study of the correlation between the clinical manifestations of the inflammatory periodontal diseases and the microbiome of periodontal pathogenic microflora in young representatives of a mixed population of the European region

2021 ◽  
Vol 18 (4) ◽  
pp. 433-444
Author(s):  
E. A. Tikhomirova ◽  
I. V. Zudina ◽  
E. S. Slazhneva ◽  
L. Yu. Orekhova ◽  
Yu. L. Denisova ◽  
...  
Keyword(s):  
Young People ◽  
Periodontal Diseases ◽  
Clinical Manifestations ◽  
Plaque Formation ◽  
Periodontal Pocket ◽  
Purulent Discharge ◽  
Control Group ◽  
Periodontal Pathogens ◽  
Dental Biofilm ◽  
Pd Complexes

The age of inflammatory periodontal disease (PD) manifestations has tended to decrease over the past decades. The study of the range of periodontal pathogens in young people and their influence on the PD manifestation contributes to the predictor identification for the early prevention of this pathology.The aim was to study the correlation between the range of periodontal pathogens in the dentoalveolar sulcus/periodontal pocket (DS/PC) contents and the clinical PD manifestations in young people.We examined 28 patients (23.1 ± 0.93 years) with dental biofilm-induced gingivitis (BG), 24 patients (30.7 ± 0.6 years) with aggressive periodontitis (AgP), and 87 clinically periodontally healthy patients (21.1 ± 0.49 years) (Control). The hygiene index and the periodontal status were determined in all patients. DNA of five periodontal pathogens was identified by PCR in the DS/PC contents. The statistical analysis was performed in Statistica 13.3. The critical significance level was p ≤ 0.05.DNA was not observed in 60.9 % of the control group samples and 7.1 % of the BG group samples. In other cases, the bacteria were found separately and as part of bacterial complexes. P.g. and T.f. were most often detected in all groups. P.g. (U = 474, р < 0.01) and A.a. (U = 209, р >< 0.05) significantly contributed to the plaque formation in the control group, T.d. – in BG and AgP groups (U = 37.5, р >< 0.05 and U = 34, р >< 0.05, respectively). In the AgP group, purulent discharge was more often recorded if T.d. was detected in the PC contents (χ2  = 5.53, р >< 0.05). T.f. + P.i. and P.g. + T.f. + P.i. complexes were exclusively associated with PD. Complexes of four bacteria were found only in the AgP group. The association of periodontal pathogens and their complexes with different PD forms was revealed.>< 0.01) and A.a. (U = 209, р <0.05) significantly contributed to the plaque formation in the control group, T.d. – in BG and AgP groups (U = 37.5, р <0.05 and U = 34, р <0.05, respectively). In the AgP group, purulent discharge was more often recorded if T.d. was detected in the PC contents (χ2  = 5.53, р <0.05). T.f. + P.i. and P.g. + T.f. + P.i. complexes were exclusively associated with PD. Complexes of four bacteria were found only in the AgP group.The association of periodontal pathogens and their complexes with different PD forms was revealed.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

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