scholarly journals Molecular profiling of microbiota in human oral cavity, stomach and intestine

2018 ◽  
Author(s):  
Qianqian Liu ◽  
Feizhou Zhu ◽  
Liyu Chen ◽  
Meihua Xu ◽  
Jianwei Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gastric Juice ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Rrna Gene ◽  
Human Oral Cavity ◽  
Stool Microbiota ◽  
The 16S Rrna Gene

The microbiota in the human gut is not only a complicated microecological system but also plays important roles in both health and disease. In order to understand the roles of these gut bacteria, we determined the distribution of microbiota in different regions of the gut by sequencing the 16S rRNA gene V4 region of the bacteria in the saliva, gastric juice, and stool of healthy individuals. The 16S rRNA gene V3-V5 region sequences of saliva and stool microbiota were obtained from Human Microbiome Project (HMP) and the V4 sequence was obtained from the V3-V5 sequences by a program designed by Perl language. We found that the microbiota of the gastric juice is more similar to those in the saliva rather than that in the stool. The frequency of some taxa was significantly different among the three groups with the Streptococcus, Veillonella, Oribacterium, Selenomonas, Actinomyces, and Granulicatella most abundant in the saliva; the Prevotella, Neisseria, Actinobacillus, Treponema, and Helicobacter most abundant in the gastric juice; and the Bacteroides, Parabacteroides, Faecalibacterium, Sutterella, Ruminococcus, Oscillospira and Phascolarctobacterium most abundant in the stool. In addition, results from PICRUSt analyses suggest that the functions of microbiota in the gastric juice are more similar as those in the saliva than in the stool. Moreover, we also found that the membrane transport of the microbiota in the saliva is higher than that in the stool and gastric juice. To our knowledge, this is the first comprehensive comparison of microbiota in the human oral cavity, stomach, and intestine.

scholarly journals Molecular profiling of microbiota in human oral cavity, stomach and intestine

2018 ◽  
Author(s):  
Qianqian Liu ◽  
Feizhou Zhu ◽  
Liyu Chen ◽  
Meihua Xu ◽  
Jianwei Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gastric Juice ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Rrna Gene ◽  
Human Oral Cavity ◽  
Stool Microbiota ◽  
The 16S Rrna Gene

The microbiota in the human gut is not only a complicated microecological system but also plays important roles in both health and disease. In order to understand the roles of these gut bacteria, we determined the distribution of microbiota in different regions of the gut by sequencing the 16S rRNA gene V4 region of the bacteria in the saliva, gastric juice, and stool of healthy individuals. The 16S rRNA gene V3-V5 region sequences of saliva and stool microbiota were obtained from Human Microbiome Project (HMP) and the V4 sequence was obtained from the V3-V5 sequences by a program designed by Perl language. We found that the microbiota of the gastric juice is more similar to those in the saliva rather than that in the stool. The frequency of some taxa was significantly different among the three groups with the Streptococcus, Veillonella, Oribacterium, Selenomonas, Actinomyces, and Granulicatella most abundant in the saliva; the Prevotella, Neisseria, Actinobacillus, Treponema, and Helicobacter most abundant in the gastric juice; and the Bacteroides, Parabacteroides, Faecalibacterium, Sutterella, Ruminococcus, Oscillospira and Phascolarctobacterium most abundant in the stool. In addition, results from PICRUSt analyses suggest that the functions of microbiota in the gastric juice are more similar as those in the saliva than in the stool. Moreover, we also found that the membrane transport of the microbiota in the saliva is higher than that in the stool and gastric juice. To our knowledge, this is the first comprehensive comparison of microbiota in the human oral cavity, stomach, and intestine.

scholarly journals Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata

2011 ◽  
Vol 61 (1) ◽  
pp. 25-29 ◽  
Author(s):  
Julia Downes ◽  
Maria Mantzourani ◽  
David Beighton ◽  
Samuel Hooper ◽  
Melanie J. Wilson ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Lipid Analysis ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Oral Cavity

Six strains of anaerobic, pleomorphic Gram-positive bacilli, isolated from the human oral cavity and an infected arm wound, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed that the isolates were most closely related to Scardovia inopinata CCUG 35729T (94.8–94.9 % 16S rRNA gene sequence similarity). The isolates were saccharolytic and produced acetic and lactic acids as end products of fermentation. The major fatty acids were C16 : 0 (49.8 %) and C18 : 1 ω9c (35.8 %). Polar lipid analysis revealed a variety of glycolipids, diphosphatidylglycerol, an unidentified phospholipid and an unidentified phosphoglycolipid. No respiratory quinones were detected. The peptidoglycan was of the type A4α l-Lys–Thr–Glu, with l-lysine partially replaced by l-ornithine. The DNA G+C content of one of the strains, C1A_55T , was 55 mol%. A novel species, Scardovia wiggsiae sp. nov., is proposed to accommodate the six isolates, with the type strain C1A_55T (=DSM 22547T=CCUG 58090T).

Metagenomic analysis of the canine oral cavity as revealed by high-throughput pyrosequencing of the 16S rRNA gene

2013 ◽  
Vol 162 (2-4) ◽  
pp. 891-898 ◽  
Author(s):  
Amy Sturgeon ◽  
Jason W. Stull ◽  
Marcio C. Costa ◽  
J. Scott Weese
Keyword(s):  
16S Rrna ◽  
Oral Cavity ◽  
16S Rrna Gene ◽  
High Throughput ◽  
Metagenomic Analysis ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures

2021 ◽  
Author(s):  
Qiyun Zhu ◽  
Shi Huang ◽  
Antonio Gonzalez ◽  
Imran McGrath ◽  
Daniel McDonald ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomics ◽  
Biologically Relevant ◽  
Metagenome Analysis ◽  
Host Sex

We introduce Operational Genomic Unit (OGU), a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent from taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldomly applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in one synthetic and two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome datasets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project dataset, and more accurate prediction of human age by the gut microbiomes in the Finnish population. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate OGU adoption in future metagenomics studies.

scholarly journals The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science

2017 ◽  
Vol 66 (2) ◽  
pp. 184-197 ◽  
Author(s):  
Nancy J. Ames ◽  
Alexandra Ranucci ◽  
Brad Moriyama ◽  
Gwenyth R. Wallen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Human Microbiome ◽  
Rrna Gene ◽  
Nursing Science ◽  
The 16S Rrna Gene

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

scholarly journals Diagnosis of Fulminant Pneumonia Caused by Legionella pneumophila Serogroup 8 with the Sequence Analysis of the 16S rRNA Gene

2011 ◽  
Vol 225 (1) ◽  
pp. 65-69 ◽  
Author(s):  
Toshinori Kawanami ◽  
Kazuhiro Yatera ◽  
Kazumasa Fukuda ◽  
Kei Yamasaki ◽  
Masamizu Kunimoto ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Legionella Pneumophila ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals The Western Progression of Lyme Disease: Infectious and NonclonalBorrelia burgdorferi Sensu LatoPopulations in Grand Forks County, North Dakota

2014 ◽  
Vol 81 (1) ◽  
pp. 48-58 ◽  
Author(s):  
Brandee L. Stone ◽  
Nathan M. Russart ◽  
Robert A. Gaultney ◽  
Angela M. Floden ◽  
Jefferson A. Vaughan ◽  
...  
Keyword(s):  
Lyme Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
North Dakota ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Content Type ◽  
Intergenic Spacer Region ◽  
Grand Forks ◽  
The 16S Rrna Gene

ABSTRACTScant attention has been paid to Lyme disease,Borrelia burgdorferi,Ixodes scapularis, or reservoirs in eastern North Dakota despite the fact that it borders high-risk counties in Minnesota. Recent reports ofB. burgdorferiandI. scapularisin North Dakota, however, prompted a more detailed examination. Spirochetes cultured from the hearts of five rodents trapped in Grand Forks County, ND, were identified asB. burgdorferi sensu latothrough sequence analyses of the 16S rRNA gene, the 16S rRNA gene-ileTintergenic spacer region,flaB,ospA,ospC, andp66. OspC typing revealed the presence of groups A, B, E, F, L, and I. Two rodents were concurrently carrying multiple OspC types. Multilocus sequence typing suggested the eastern North Dakota strains are most closely related to those found in neighboring regions of the upper Midwest and Canada. BALB/c mice were infected withB. burgdorferiisolate M3 (OspC group B) by needle inoculation or tick bite. Tibiotarsal joints and ear pinnae were culture positive, andB. burgdorferiM3 was detected by quantitative PCR (qPCR) in the tibiotarsal joints, hearts, and ear pinnae of infected mice. Uninfected larvalI. scapularisticks were able to acquireB. burgdorferiM3 from infected mice; M3 was maintained inI. scapularisduring the molt from larva to nymph; and further, M3 was transmitted from infectedI. scapularisnymphs to naive mice, as evidenced by cultures and qPCR analyses. These results demonstrate that isolate M3 is capable of disseminated infection by both artificial and natural routes of infection. This study confirms the presence of unique (nonclonal) and infectiousB. burgdorferipopulations in eastern North Dakota.

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