<i>Leptotrichia</i> species in human infections II

Eribe, Emenike Ribs K.; Olsen, Ingar

doi:10.1080/20002297.2017.1368848

Cited by 115 publications

(95 citation statements)

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“…Among genera usually reported as part of the normal flora of the gastrointestinal tract, only Veillonella is found regularly at other sites, like the mouth 77 . Leptotrichia species mostly colonize the oral cavity and they were isolated from various human infections, suggesting that they are emerging human pathogens 78,79 . Oribacterium also inhabits the mouth, besides the upper respiratory tract 80 .…”

Section: Resultsmentioning

confidence: 99%

Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment orHelicobacter pyloriinfection

Ciucci

Durán

Palladini

et al. 2020

Preprint

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40Although long thought to be a sterile and inhospitable environment, the stomach is inhabited 41 by diverse microbial communities, co-existing in a dynamic balance. Long-term use of orally 42 administered drugs such as Proton Pump Inhibitors (PPIs), or bacterial infection such as 43 Helicobacter pylori, cause significant microbial alterations. Yet, studies revealing how the 44 commensal bacteria re-organize, due to these perturbations of the gastric environment, are in 45 the early phase. They mainly focus on the most prevalent taxa and rely on linear techniques for 46 multivariate analysis. 47Here we disclose the importance of complementing linear dimensionality reduction techniques 48 such as Principal Component Analysis and Multidimensional Scaling with nonlinear 49 approaches derived from the physics of complex systems. Then, we show the importance to 50 complete multivariate pattern analysis with differential network analysis, to reveal mechanisms 51 of re-organizations which emerge from combinatorial microbial variations induced by a 52 medical treatment (PPIs) or an infectious state (H. pylori). 53 Keywords 54 Proton Pump Inhibitors -Dyspepsia -Helicobacter pylori -Gastric microbiota -Linear and 55 nonlinear unsupervised methods -Mininum Curvilinear Embedding -Nonlinearity -PC-corr 56 network -16S rRNA 57 58 3 Introduction 59The gastric environment with its microbiota is the active gate that regulates access to the whole 60 gastrointestinal tract, and therefore it has a remarkable impact on the correct functionality of 61 the entire human organism. Recent studies have revealed that many orally administered drugs 62 can perturb the elegant balance of the gastric flora 1,2 . However, not all of them cause permanent 63 adverse effects and particular attention should be addressed to drugs that are frequently 64 prescribed and administered for long periods. They can cause permanent unbalance of the 65 gastric microbiota that might generate adverse side effects for the patient's health. Since the 66 introduction of proton pump inhibitors (PPIs) into clinical practice more than 25 years ago, PPIs 67 have become the mainstay in the treatment of gastric-acid-related diseases 3 . PPIs are potent 68 agents that block acid secretion by gastric parietal cells by binding covalently to and inhibiting 69 the hydrogen/potassium (H + /K + )-ATPases (or proton pumps), and additionally they can bind 70 non-gastric H + /K + -ATPases, both on human cells and on bacteria and fungi, such as 71 Helicobacter pylori (H. pylori) 4-6 . 72 PPIs are drugs of first choice for peptic ulcers (PU) and their complications (e.g. bleeding), 73 gastroesophageal reflux disease (GERD), nonsteroidal anti-inflammatory drug (NSAID)-74 induced gastrointestinal (GI) lesions, Zollinger-Ellison syndrome and dyspepsia 3,7,8 . In 75 particular, dyspepsia is a common clinical problem characterized by symptoms (e.g. epigastric 76 pain, burning, postprandial fullness, or early satiation) originating from the gastroduodenal 77 region 9 . The potent gastri...

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Section: Resultsmentioning

confidence: 99%

Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment orHelicobacter pyloriinfection

Ciucci

Durán

Palladini

et al. 2020

Preprint

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“…The species within the family Leptotrichiaceae, order Fusobacteriales, are large, fusiform, non-sporulating and nonmotile rods or coccobacilli with a Gram-negative-like cell wall [1,2]. The species are mainly capnophilic or anaerobic, especially on first isolation, but many strains subsequently grow aerobically in the presence of CO 2 [2].…”

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Oceanivirga miroungae sp. nov., isolated from oral cavity of northern elephant seal (Mirounga angustirostris)

Volokhov

Blom

Amselle

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Two independent strains of a Leptotrichia species (ES3154-GLUT and ES2714_GLU) were isolated from the oral cavity of northern elephant seals (Mirounga angustirostris) that were admitted to The Marine Mammal Centre facilities in California, USA. The strains were isolated from oral swabs by cultivation in PPLO broth supplemented with serum, penicillin and colistin in anaerobic conditions. The strains were Gram-negative, pleomorphic, indole-, oxidase- and catalase-negative, non-spore-forming, non-motile rods/coccobacilli in short chains. The 16S rRNA gene sequence of these strains shared 94.42 % nucleotide similarity with Oceanivirga salmonicida AVG 2115T but demonstrated ≤86.00–92.50 % nucleotide similarity to the 16S rRNA genes of other species of the family Leptotrichiaceae . The genome was sequenced for strain ES3154-GLUT. Average nucleotide identity values between strain ES3154-GLUT and 15 type strain genomes from the family Leptotrichiaceae ranged from 66.74 % vs. Sebaldella termitidis to 73.35 % vs. O. salmonicida . The whole genome phylogeny revealed that the novel species was most closely related to O. salmonicida AVG 2115T. This relationship was also confirmed by nucleotide similarity and multilocus phylogenetic analyses employing various housekeeping genes (partial 23S rRNA, rpoB, rpoC, rpoD, polC, adh, gyrA and gyrB genes). Chemotaxonomic and phenotypical features of strain ES3154-GLUT were in congruence with closely related members of the family Leptotrichiaceae , represented by similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis was capable to clearly discriminate strain ES3154-GLUT from all currently described taxa of the family Leptotrichiaceae . Based on these data, we propose a novel species of the genus Oceanivirga , for which the name Oceanivirga miroungae sp. nov. is proposed with the type strain ES3154-GLUT (=DSM 109740T=CCUG 73653T=ATCC TSD-189T=NCTC 14411T) and one representative strain ES2714_GLU. The G+C content is 26.82 %, genome size is 1 356 983 bp.

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“…in various infectious diseases has gained considerable attention (Eribe and Olsen, 2017). However, the exact clinical impact of Leptotrichia species relevant to infectious diseases remains unclear due to difficulties in bacterial culture, isolation and identification.…”

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confidence: 99%

“…To date, eight Leptotrichia species have been characterised, which include L. buccalis, L. goodfellowii, L. hofstadii, L. shahii, L. trevisanii, L. massiliensis, L. hongkongensis and L. wadei. However, many clinical Leptotrichia isolates have remained unclassified due to the lack of the whole-genome sequences and biochemical properties of these isolates (Eribe and Olsen, 2017). Currently, Leptotrichia genome data are very limited as there are only one complete whole genome sequences of species-identified strain and three unidentified strains available in the GenBank database (Gupta and Sethi, 2014;Ivanova et al, 2009).…”

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confidence: 99%

“…To date, eight species of Leptotrichia have been precisely described(Eribe et al, 2004;Woo et al, 2010). Apart from the eight Leptotrichia species, previous analysis based on the 16S rRNA gene identified 10 unclassified Leptotrichia species, indicating that some Leptotrichia strains have not yet being assigned a species name(Eribe and Olsen, 2008;Eribe and Olsen, 2017). Species classification based on both phenotype and genotype is an essential starting point to understand the biology, ecology and clinical impacts of Leptotrichia species.…”

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Composition and Diversity of CRISPR-Cas13a systems in the genus Leptotrichia

Watanabe

Cui

Kiga

et al. 2019

Preprint

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Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNAtargeting CRISPR-Cas system and has the unique characteristics of both targeted and collateral single-stranded RNA (ssRNA) cleavage activities, which was first identified in Leptotrichia shahii CRISPR-Cas13a. Here, the complete whole genome sequences of 11Leptotrichia strains were determined and compared with 18 publicly available Leptotrichia genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a and other CRISPR-Cas systems. Various types of CRISPR-Cas systems,

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Leptotrichia species in human infections II

Cited by 115 publications

References 100 publications

Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment orHelicobacter pyloriinfection

Machine learning pattern recognition and differential network analysis of gastric microbiome in the presence of proton pump inhibitor treatment orHelicobacter pyloriinfection

Oceanivirga miroungae sp. nov., isolated from oral cavity of northern elephant seal (Mirounga angustirostris)

Composition and Diversity of CRISPR-Cas13a systems in the genus Leptotrichia

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