Genome sequence and description of Blautia brookingsii str SG772 nov., a new species of anaerobic bacterium isolated from healthy human gut

AbstractStrain SG-772 is a Gram positive, strictly anoxic bacterium isolated from the feces of a healthy human fecal donor. Based on 16S rRNA gene sequence, the strain showed maximum similarity (94.39%) with Blautia stercoris GAM6-1 in EZ-Taxon server and thus assigned the genus Blautia. The scanning electron micrograph of the bacterium revealed the characteristic coccobacillus shape as well as the complete absence of flagellum, suggesting its non-motile phenotype. This strain was found to utilize 27 substrates based on Biolog AN plates assay, with maximum preference for D-mannitol. Additionally, the strain was found to be resistant to tetracycline and streptomycin. Genome sequencing and analysis revealed an overall genome size of 3.49 Mbp and GC content of 43.97%. Based on RAST annotation server, the closest neighbor was Blautia hansenii DSM20583. Average Nucleotide Identity (ANI) of these strains were 81.69%, suggesting a high level of genomic variation. The comparative genome analysis of strain SG772 with B. hansenii DSM20583 revealed a total of 411 orthologous genes coding for basic metabolic functions. Furthermore, the genomes were functionally distinct based on COG categories. Thus, based on all these differences, we propose a novel species of genus Blautia named as Blautia brookingsii SG772.

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Complete genome sequence of Chryseobacterium sp. ZHDP1 with protease activity

10.21203/rs.3.rs-581195/v1 ◽

2021 ◽

Author(s):

Huanshuai Zhao ◽

Jianxin Wang ◽

Jiamao Huang ◽

Yuncheng Ma ◽

Yunfei Chen ◽

...

Keyword(s):

Complete Genome ◽

Protease Activity ◽

Fermentation Broth ◽

Gc Content ◽

Rrna Genes ◽

Trna Genes ◽

Rrna Gene ◽

The Novel ◽

Maximum Similarity ◽

Insight Into

Abstract This study reported a complete genome of Chryseobacterium sp. ZHDP1 isolated from the soils of a seafood market. The ZHDP1 genome with a size of 4,917,748 bp and a GC content of 35.95% possessed 4,478 coding genes, 5 rRNA genes, 26 sRNA genes, and 89 tRNA genes. The 16S rRNA gene sequence of ZHDP1 had a maximum similarity of 99.07% with that of C. gambrini 5-1St1a. The maximum values of average nucleotide identity and DNA-DNA hybridization of ZHDP1 genome were 91.39 and 47.8, respectively, which were lower than the thresholds for a new genome. Different protease genes were annotated in the genome of ZHDP1, and the protease activity was also detected in the fermentation broth of ZHDP1. Furthermore, the activity of protease in the fermentation broth was optimized through temperature, pH, and metal irons, and the results showed that 60°C and pH 7.0 were the optimum conditions and Fe3+ could positively increase the protease activity of ZHDP1. This study provides the first insight into the novel genomic information of Chryseobacterium sp. ZHDP1 and its protein-degrading ability, thereby broadening our knowledge of the industrial potentials in genus Chryseobacterium strains.

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Stable Engraftment of a Human Gut Bacterial Microbiome in Double Humanized BLT-mice

10.1101/749093 ◽

2019 ◽

Cited By ~ 1

Author(s):

Lance Daharsh ◽

Amanda E. Ramer-Tait ◽

Qingsheng Li

Keyword(s):

Immune System ◽

Gut Microbiome ◽

Human Disease ◽

Humanized Mice ◽

Rrna Gene ◽

Human Immune System ◽

Human Gut ◽

Healthy Human ◽

Human Immune

AbstractBackgroundHumanized mice featuring a functional human immune system are an important pre-clinical model for examining immune responses to human-specific pathogens. This model has been widely utilized to study human diseases that are otherwise impossible or difficult to investigate in humans or with other animal models. However, one limitation of using humanized mice is their native murine gut microbiome, which significantly differs from the one found in humans. These differences may be even greater for mice housed and bred in specific pathogen free conditions. Given the importance of the gut microbiome to human health and disease, these differences may profoundly impact the ability to translate the results from humanized mice studies to human disease. Further, there is a critical need for improved pre-clinical models to study the complex in vivo relationships of the gut microbiome, immune system, and human disease. We therefore created double humanized mice with both a functional human immune system and stable human-like gut microbiome.ResultsSurgery was performed on NOD.Cg-PrkdcscidII2rgtm1Wjl/SzJ (NSG) mice to create bone-marrow, liver, thymus (BLT) humanized mice. After immune reconstitution, mice were treated with broad spectrum antibiotics to deplete murine gut bacteria and then transplanted with fecal material from healthy human donors. Characterization of 173 fecal samples obtained from 45 humanized mice revealed that double humanized mice had unique 16S rRNA gene profiles consistent with those of the individual human donor samples. Importantly, transplanted human-like gut microbiomes were stable in mice for the duration of the study, up to 14.5 weeks post-transplant. Microbiomes of double humanized mice also harbored predicted functional capacities that more closely resembled those of the human donors compared to humanized mice.ConclusionsHere, we describe successful engraftment of a stable human microbiome in BLT humanized mice to further improve this preclinical humanized mouse model. These double humanized mice represent a unique and tractable new model to study the complex relationships between the human gut microbiome, human immune system, and human disease in vivo.

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Analysis of Human Gut Microbiome: Taxonomy and Metabolic Functions in Thai Adults

Genes ◽

10.3390/genes12030331 ◽

2021 ◽

Vol 12 (3) ◽

pp. 331

Author(s):

Nachon Raethong ◽

Massalin Nakphaichit ◽

Narissara Suratannon ◽

Witida Sathitkowitchai ◽

Wanlapa Weerapakorn ◽

...

Keyword(s):

Gut Microbiome ◽

Asian Country ◽

Rrna Gene ◽

Metagenomic Sequencing ◽

Sequencing Data ◽

Human Gut ◽

Thai Population ◽

Shotgun Metagenomics ◽

Human Gut Microbiome ◽

Metabolic Functions

The gut microbiome plays a major role in the maintenance of human health. Characterizing the taxonomy and metabolic functions of the human gut microbiome is necessary for enhancing health. Here, we analyzed the metagenomic sequencing, assembly and construction of a meta-gene catalogue of the human gut microbiome with the overall aim of investigating the taxonomy and metabolic functions of the gut microbiome in Thai adults. As a result, the integrative analysis of 16S rRNA gene and whole metagenome shotgun (WMGS) sequencing data revealed that the dominant gut bacterial families were Lachnospiraceae and Ruminococcaceae of the Firmicutes phylum. Consistently, across 3.8 million (M) genes annotated from 163.5 gigabases (Gb) of WMGS sequencing data, a significant number of genes associated with carbohydrate metabolism of the dominant bacterial families were identified. Further identification of bacterial community-wide metabolic functions promisingly highlighted the importance of Roseburia and Faecalibacterium involvement in central carbon metabolism, sugar utilization and metabolism towards butyrate biosynthesis. This work presents an initial study of shotgun metagenomics in a Thai population-based cohort in a developing Southeast Asian country.

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MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008487 ◽

2021 ◽

Vol 17 (1) ◽

pp. e1008487

Author(s):

Preecha Patumcharoenpol ◽

Massalin Nakphaichit ◽

Gianni Panagiotou ◽

Anchalee Senavonge ◽

Narissara Suratannon ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gut Microbiome ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Functional Capability ◽

Human Gut ◽

Human Gut Microbiome ◽

Metabolic Functions ◽

Scale Models

Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.

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Phenotypic and Molecular Characterization of Lactobacilli Isolated from breast-fed Infants faeces in Bechar region,South West of Algeria

South Asian Journal of Experimental Biology ◽

10.38150/sajeb.8(6).p212-221 ◽

2019 ◽

Vol 8 (6) ◽

pp. 212-221

Author(s):

Yagoubi Ahmed ◽

Bensoltane Ahmed

Keyword(s):

Lipolytic Activity ◽

Lactic Acid Production ◽

Lactobacillus Rhamnosus ◽

Rrna Gene ◽

Healthy Human ◽

Maximum Acidity ◽

Infant Feces ◽

High Level ◽

Reconstituted Milk ◽

First Time

Lactobacilli are of great importance to humans, as they are essential members of a healthy human microbiota at various niches and serve as biologically and functionally important components of a healthy human diet. For this reason, the isolation of lactobacilli strains from infant feces (less than 6 months old) was carried out in Bechar region, Algeria. In total, 62 strains were isolated, purified, and identified based on the physiological and biochemical methods. For final confirmation, API 50 CHL gallery was used. The iden ca on and phylogenetic analysis of isolated strains was performed by sequencing the 16S rRNA gene, which led us to identify four species with different percentages; Lactobacillus rhamnosus, L. fermentum, L.mucosa, L. plantarum. With regard to the characteristics of technological interest, most of the identified strains exhibited good lactic acid production. However, it was not until after 3 hours of incubation at 37 °C that isolated lactobacilli produced a maximum acidity, which reached Δ pH 0.54 in the reconstituted milk. The results were different with camel milk, in the first time, and this was observed in the acidity rate which was generally lower in this type of milk in which acidity reached Δ pH 0.47 .As regards the proteolytic power, the strains showed a high level of proteolysis. Regarding the lipolytic activity, it was observed that none of the lactobacilli tested expressed lipolytic activity in the presence of buffer and olive oil, whereas the results of the strains were different as regards the flavoring activity and the texturing activity.

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Collinsella provencensis sp. nov., a new species identified from healthy human gut microbiota.

10.21203/rs.3.rs-197616/v1 ◽

2021 ◽

Author(s):

Sarah BENABDELKADER ◽

Cheikh Ibrahima LO ◽

Sabrina NAUD ◽

Niokhor DIONE ◽

Stéphane ALIBAR ◽

...

Keyword(s):

New Species ◽

Ribosomal Rna ◽

Gene Sequence ◽

Cellular Fatty Acid ◽

Biochemical Properties ◽

The Novel ◽

Human Gut ◽

Healthy Human ◽

Gene Sequence Analysis ◽

A New Species

Abstract A Gram-positive and anaerobic bacterium was isolated from the stool sample of a healthy French volunteer. A taxonogenomics approach was adopted to characterize it. Cells are rod shaped non-spore-forming and non-motile. Growth of strain Marseille-P3740 occurs at 37°C in anaerobic atmosphere at pH 7. The 16S ribosomal RNA gene sequence analysis of the novel strain Marseille-P3740 displayed 96.31% similarity in nucleotide sequence with Collinsella intestinalis strain JCM 10643, the phylogenetically closest related species with standing in nomenclature. C16:0, C18:1n9 and C18:2n6 are the major cellular fatty acid components. The genomic of strain Marseille-P3740T is 1.74 Mbp long with 59.1 mol% of G + C content. Based on the taxonogenomic description and the phenotypic and biochemical properties of this bacterium, we propose the strain Marseille-P3740T (= CSUR P3740 = CCUG 70947) as a new species, Collinsella provencensis sp. nov.

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Genetic and morphological differentiation of Mosor rock lizards, Dinarolacerta mosorensis (Kolombatović, 1886), with the description of a new species from the Prokletije Mountain Massif (Montenegro) (Squamata: Lacertidae)

Zootaxa ◽

10.11646/zootaxa.1613.1.1 ◽

2007 ◽

Vol 1613 (1) ◽

pp. 1-22 ◽

Cited By ~ 6

Author(s):

KATARINA LJUBISAVLJEVIĆ ◽

OSCAR ARRIBAS ◽

GEORG DšUKIĆ ◽

SALVADOR CARRANZA

Keyword(s):

New Species ◽

Morphological Differentiation ◽

Balkan Peninsula ◽

12S Rrna ◽

Rrna Gene ◽

Lacertid Lizard ◽

12S Rrna Gene ◽

Mitochondrial 12S Rrna ◽

High Level ◽

A New Species

A new species of lacertid lizard of the genus Dinarolacerta is described from the Prokletije Mountain Massif, Montenegro. This new species, Dinarolacerta montenegrina sp. nov., is characterized by its relatively small size, by usually having only one postnasal scale on one or on both sides of the head, a relatively lower number of temporal and postocular scales and a relatively high number of ventral scales. Osteologically, it is mainly characterized by the complete absence of the anteromedial process in the postocular bone, and more reduced supraocular osteoderms. The phylogenetic analysis using partial sequences of the mitochondrial 12S rRNA gene supports the specific status of D. montenegrina sp. nov. and shows that it represents an old independent lineage that separated from its sister species, D. mosorensis, in the late Miocene. The Morača river canyon may have acted as a geomorphological and climatic barrier causing the speciation between the two species of Dinarolacerta. The discovery of this new species endemic to the Balkan Peninsula highlights the importance of the Dinarides as one of the main European hotspots of biodiversity. This high level of endemicity in the Dinaric region is probably the result of both its geographic situation and its complex geological history and morphology.

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Healthy human gut phageome

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1601060113 ◽

2016 ◽

Vol 113 (37) ◽

pp. 10400-10405 ◽

Cited By ~ 230

Author(s):

Pilar Manrique ◽

Benjamin Bolduc ◽

Seth T. Walk ◽

John van der Oost ◽

Willem M. de Vos ◽

...

Keyword(s):

Gut Microbiome ◽

Healthy Individuals ◽

Human Gut ◽

Healthy Human ◽

Irritable Bowel Disease ◽

Irritable Bowel ◽

High Level ◽

And Function ◽

Globally Distributed

The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20–50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.

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Association between 16S rRNA gene mutations and susceptibility to amikacin in Mycobacterium avium Complex and Mycobacterium abscessus clinical isolates

Scientific Reports ◽

10.1038/s41598-021-85721-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Su-Young Kim ◽

Dae Hun Kim ◽

Seong Mi Moon ◽

Ju Yeun Song ◽

Hee Jae Huh ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Mycobacterium Avium ◽

Inhibitory Concentration ◽

Gene Mutations ◽

Mycobacterium Abscessus ◽

Clinical Isolates ◽

Rrna Gene ◽

High Level ◽

Culture Conversion

AbstractWe evaluated the association between 16S rRNA gene (rrs) mutations and susceptibility in clinical isolates of amikacin-resistant nontuberculous mycobacteria (NTM) in NTM-pulmonary disease (PD) patients. Susceptibility was retested for 134 amikacin-resistant isolates (minimum inhibitory concentration [MIC] ≥ 64 µg/ml) from 86 patients. Amikacin resistance was reconfirmed in 102 NTM isolates from 62 patients with either Mycobacterium avium complex-PD (MAC-PD) (n = 54) or M. abscessus-PD (n = 8). MICs and rrs mutations were evaluated for 318 single colonies from these isolates. For the 54 MAC-PD patients, rrs mutations were present in 34 isolates (63%), comprising all 31 isolates with amikacin MICs ≥ 128 µg/ml, but only three of 23 isolates with an MIC = 64 µg/ml. For the eight M. abscessus-PD patients, all amikacin-resistant (MIC ≥ 64 µg/ml) isolates had rrs mutations. In amikacin-resistant isolates, the A1408G mutation (n = 29) was most common. Two novel mutations, C1496T and T1498A, were also identified. The culture conversion rate did not differ by amikacin MIC. Overall, all high-level and 13% (3/23) of low-level amikacin-resistant MAC isolates had rrs mutations whereas mutations were present in all amikacin-resistant M. abscessus isolates. These findings are valuable for managing MAC- and M. abscessus-PD and suggest the importance of phenotypic and genotypic susceptibility testing.

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Molecular pathways to high-level azithromycin resistance in Neisseria gonorrhoeae

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkab084 ◽

2021 ◽

Cited By ~ 1

Author(s):

J G E Laumen ◽

S S Manoharan-Basil ◽

E Verhoeven ◽

S Abdellati ◽

I De Baetselier ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Ribosomal Proteins ◽

Efflux Pump ◽

23S Rrna ◽

Rrna Gene ◽

23S Rrna Gene ◽

Evolution Of Resistance ◽

High Level ◽

Azithromycin Resistance ◽

Level Resistance

Abstract Background The prevalence of azithromycin resistance in Neisseria gonorrhoeae is increasing in numerous populations worldwide. Objectives To characterize the genetic pathways leading to high-level azithromycin resistance. Methods A customized morbidostat was used to subject two N. gonorrhoeae reference strains (WHO-F and WHO-X) to dynamically sustained azithromycin pressure. We tracked stepwise evolution of resistance by whole genome sequencing. Results Within 26 days, all cultures evolved high-level azithromycin resistance. Typically, the first step towards resistance was found in transitory mutations in genes rplD, rplV and rpmH (encoding the ribosomal proteins L4, L22 and L34 respectively), followed by mutations in the MtrCDE-encoded efflux pump and the 23S rRNA gene. Low- to high-level resistance was associated with mutations in the ribosomal proteins and MtrCDE efflux pump. However, high-level resistance was consistently associated with mutations in the 23S ribosomal RNA, mainly the well-known A2059G and C2611T mutations, but also at position A2058G. Conclusions This study enabled us to track previously reported mutations and identify novel mutations in ribosomal proteins (L4, L22 and L34) that may play a role in the genesis of azithromycin resistance in N. gonorrhoeae.

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