A rod-shaped and Gram-stain-negative bacterial strain 9AT, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9AT belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9AT is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9AT is MK-7 and the major fatty acids comprise Summed Feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 25.2 %), iso-C15 : 0 (23.2 %), C16 : 1 ω5c (11.6 %), Summed Feature 4 (anteiso-C17 : 1 B/iso-C17 : 1 I) (9.6 %) and anteiso-C15 : 0 (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern sym-homospermidine is predominant. On the basis of the results obtained, strain 9AT is proposed as a novel species of the genus Hymenobacter, for which the name Hymenobacter caeli sp. nov. is suggested. The type strain is 9AT (=CCM 8971T=LMG 32109T=DSM 111653T).
- MeSH
- Bacteroidetes klasifikace genetika izolace a purifikace MeSH
- DNA bakterií genetika MeSH
- fylogeneze MeSH
- genom bakteriální MeSH
- mikrobiologie vzduchu * MeSH
- ostrovy * MeSH
- pravděpodobnostní funkce MeSH
- RNA ribozomální 16S genetika MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Antarktida MeSH
- ostrovy * MeSH
A group of thirteen bacterial strains was isolated from rock samples collected in a deglaciated northern part of James Ross Island, Antarctica. The cells were rod-shaped, Gram-stain-negative, non-motile, catalase positive, and produced moderately slimy, ultraviolet light (UVC)-irradiation-resistant and red-pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, extensive biotyping, fatty acid profile, chemotaxonomy analyses, and whole genome sequencing were applied in order to clarify the taxonomic position of these isolates. Phylogenetic analysis based on the 16S rRNA gene indicated that all isolates constituted a coherent group belonging to the genus Hymenobacter. The closest relatives to the representative isolate P5136T were Hymenobacter psychrophilus BZ33rT and Hymenobacter rubripertinctus CCM 8852T, exhibiting 97.53% and 97.47% 16S rRNA pairwise similarity, respectively. Average nucleotide identity calculated from the whole-genome sequencing data supported the finding that P5136T represents a distinct Hymenobacter species. The major components in fatty acid profiles were Summed Feature 3 (C16:1ω7c/C16:1ω6c), C16:1ω5c, C15:0 iso and C15:0 anteiso. The cellular quinone content contained unanimously menaquinone MK-6 and MK-7 (ratio 1:5.1). The predominant polar lipid was phosphatidylethanolamine, and moderate to minor amounts of two unknown polar lipids, two unknown aminolipids, one unknown glycolipid and two unknown glycophospholipids were present. The G+C content of genomic DNAs is 60.31mol%. Based on all the obtained results, we propose a novel species for which the name Hymenobacter amundsenii sp. nov. is suggested, with the type strain P5136T (=CCM 8682T=LMG 29687T).
- MeSH
- Bacteroidetes chemie klasifikace genetika fyziologie MeSH
- chinony analýza MeSH
- DNA bakterií genetika MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- genom bakteriální genetika MeSH
- lipidy analýza MeSH
- mastné kyseliny analýza MeSH
- pigmentace MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- tolerance záření * MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Antarktida MeSH
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
- MeSH
- Bacteroidetes klasifikace genetika virologie MeSH
- bakteriofágy klasifikace genetika MeSH
- DNA virů genetika MeSH
- feces virologie MeSH
- fylogeneze MeSH
- fylogeografie MeSH
- genetická variace MeSH
- koevoluce * MeSH
- lidé MeSH
- primáti virologie MeSH
- střevní mikroflóra * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
A bacterial strain designated CCM 8645T was isolated from a soil sample collected nearby a mummified seal carcass in the northern part of James Ross Island, Antarctica. The cells were short rods, Gram-stain-negative, non-motile, catalase and oxidase positive, and produced a red-pink pigment on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, extensive biotyping using conventional tests and commercial identification kits and chemotaxonomic analyses were applied to clarify its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene placed strain CCM 8645T in the genus Mucilaginibacter with the closest relative being Mucilaginibacter daejeonensis Jip 10T, exhibiting 96.5 % 16S rRNA pairwise similarity which was clearly below the 97 % threshold value recommended for species demarcation. The major components in fatty acid profiles were Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C15 : 0 iso and C17 : 0 iso 3OH. The cellular quinone content was exclusively menaquinone MK-7. The major polyamine was sym-homospermidine and predominant polar lipids were phosphatidylethanolamine and phosphatidylserine. Based on presented results, we propose a novel species for which the name Mucilaginibacter terrae sp. nov. is suggested, with the type strain CCM 8645T (=LMG 29437T).
- MeSH
- Bacteroidetes klasifikace genetika izolace a purifikace MeSH
- DNA bakterií genetika MeSH
- fosfatidylethanolaminy chemie MeSH
- fosfatidylseriny chemie MeSH
- fylogeneze * MeSH
- mastné kyseliny chemie MeSH
- pigmentace MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- spermidin analogy a deriváty chemie MeSH
- techniky typizace bakterií MeSH
- vitamin K 2 analogy a deriváty chemie MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Antarktida MeSH
Bacteria associated with mites influence their fitness, nutrition and reproduction. Previously, we found Solitalea-like (Sphingobacteriales) and Candidatus Cardinium (Cytophagales) bacteria in the stored product mite Acarus siro L. by cloning and using pyrosequencing. In this study, taxon-specific primers targeting 16S rRNA gene were used to detect and quantify the bacteria in mites and eggs of three A. siro populations. The specific probes for fluorescent in situ hybridization (FISH) were used to localize Solitalea-like and Cardinium bacteria in mite bodies. The population growth as an indirect estimator of fitness was used to describe the mite-bacteria interactions on (1) control diet; (2) rifampicin supplemented diet; (3) tetracycline supplemented diet; (4) rifampicin pretreated mites; (5) tetracycline pretreated mites. Solitalea-like 16S rRNA gene sequences from A. siro formed a separate cluster together with sequences from Tyrophagus putrescentiae. qPCR analysis indicated that number of Solitalea-like bacteria 16S rRNA gene copies was ca. 100× higher than that of Cardinium and the numbers differed between populations. FISH analysis localized Solitalea-like bacteria in the parenchymal tissues, mesodeum and food bolus of larvae, nymphs and adults. Solitalea-like, but not Cardinium bacteria were detected by taxon-specific primers in mites and eggs of all three investigated populations. None of the antibiotic treatments eliminated Solitalea-like bacteria in the A. siro populations tested. Rifampicin pretreatment significantly decreased the population growth. The numbers of Solitalea-like bacteria did not correlate with the population growth as a fitness indicator. This study demonstrated that A. siro can host Solitalea-like bacteria either alone or together with Cardinium. We suggest that Solitalea-like bacteria are shared by vertical transfer in A. siro populations.
- MeSH
- Acaridae růst a vývoj mikrobiologie MeSH
- antibakteriální látky farmakologie MeSH
- Bacteroidetes klasifikace genetika fyziologie MeSH
- DNA bakterií genetika MeSH
- genetická zdatnost * MeSH
- hybridizace in situ fluorescenční MeSH
- krmivo pro zvířata analýza MeSH
- larva růst a vývoj mikrobiologie MeSH
- nymfa růst a vývoj mikrobiologie MeSH
- RNA ribozomální 16S genetika MeSH
- symbióza MeSH
- zvířata MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
High-grain feeding used in the animal production is known to affect the host rumen bacterial community, but our understanding of consequent changes in goats is limited. This study was therefore aimed to evaluate bacterial population dynamics during 20 days adaptation of 4 ruminally cannulated goats to the high-grain diet (grain: hay - ratio of 40:60). The dietary transition of goats from the forage to the high-grain-diet resulted in the significant decrease of rumen fluid pH, which was however still higher than value established for acute or subacute ruminal acidosis was not diagnosed in studied animals. DGGE analysis demonstrated distinct ruminal microbial populations in hay-fed and grain-fed animals, but the substantial animal-to-animal variation were detected. Quantitative PCR showed for grain-fed animals significantly higher number of bacteria belonging to Clostridium leptum group at 10 days after the incorporation of corn into the diet and significantly lower concentration of bacteria belonging to Actinobacteria phylum at the day 20 after dietary change. Taxonomic distribution analysed by NGS at day 20 revealed the similar prevalence of the phyla Firmicutes and Bacteroidetes in all goats, significantly higher presence of the unclassified genus of groups of Bacteroidales and Ruminococcaceae in grain-fed animals and significantly higher presence the genus Prevotella and Butyrivibrio in the forage-fed animals. The three different culture-independent methods used in this study show that high proportion of concentrate in goat diet does not induce any serious disturbance of their rumen ecosystem and indicate the good adaptive response of caprine ruminal bacteria to incorporation of corn into the diet.
- MeSH
- Actinobacteria klasifikace genetika metabolismus MeSH
- bachor mikrobiologie MeSH
- Bacteroidetes klasifikace genetika metabolismus MeSH
- Butyrivibrio klasifikace genetika metabolismus MeSH
- Clostridium klasifikace genetika metabolismus MeSH
- fermentace MeSH
- Firmicutes klasifikace genetika metabolismus MeSH
- fylogeneze MeSH
- fyziologie výživy zvířat * MeSH
- koncentrace vodíkových iontů MeSH
- kozy MeSH
- krmivo pro zvířata analýza MeSH
- kukuřice setá chemie metabolismus MeSH
- lipnicovité chemie metabolismus MeSH
- píštěl žaludku MeSH
- Prevotella klasifikace genetika metabolismus MeSH
- Ruminococcus klasifikace genetika metabolismus MeSH
- sekvenční analýza DNA MeSH
- střevní mikroflóra fyziologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P < 0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P < 0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 °C was found as the optimal method to study ruminal bacterial profile.
- MeSH
- bachor mikrobiologie MeSH
- Bacteroidetes klasifikace genetika izolace a purifikace MeSH
- denaturační gradientová gelová elektroforéza MeSH
- DNA bakterií izolace a purifikace MeSH
- fylogeneze MeSH
- grampozitivní bakterie klasifikace genetika izolace a purifikace MeSH
- kryoprezervace * MeSH
- kvantitativní polymerázová řetězová reakce MeSH
- odběr biologického vzorku metody MeSH
- skot MeSH
- taxonomické DNA čárové kódování * MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Bacterial clone libraries of the gut microbiota of nurtured and starved Cylindroiulus fulviceps specimens displayed the predominance of the phyla Bacteroidetes (55 and 37 %, respectively) and Proteobacteria (40 and 35 %, respectively) and a high similarity to bacteria previously detected in the intestinal tract of termites and beetles, which are known to harbor symbiotic bacteria essential for digestive activity. Bacterial isolates were dominated by Proteobacteria (74 %), followed by members of the phyla Actinobacteria, Firmicutes and Bacteroidetes. PCR-DGGE fingerprints of the gut samples showed that intestinal bacteria were affected by starvation, although the change was not significant.
- MeSH
- Actinobacteria genetika izolace a purifikace klasifikace MeSH
- Bacteria genetika izolace a purifikace klasifikace MeSH
- Bacteroidetes genetika izolace a purifikace klasifikace MeSH
- bakteriologické techniky MeSH
- členovci mikrobiologie MeSH
- DNA bakterií genetika MeSH
- DNA fingerprinting metody MeSH
- ekosystém MeSH
- elektroforéza v agarovém gelu metody MeSH
- financování organizované MeSH
- fylogeneze MeSH
- gastrointestinální trakt mikrobiologie MeSH
- klonování DNA metody MeSH
- kultivační média MeSH
- metagenom MeSH
- molekulární sekvence - údaje MeSH
- Proteobacteria genetika izolace a purifikace klasifikace MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
The influence was evaluated of post-weaning normal nutrition and over-nutrition upon the development of the intestinal microbiota, the alkaline phosphatase activity (AP) and occurrence of obesity in male Sprague-Dawley rats (from days 21 to 40 the control rats were submitted to ad libitum intake of a standard laboratory diet whereas overfed rats received the same diet supplemented with milk-based high fat liquid diet). The jejunal numbers of two dominant divisions of bacteria, i.e. Firmicutes (Lactobacillus/ Enterococcus--LAB) and the Bacteroidetes (Bacteroides/Prevotella--BAC), were determined using the fluorescent in situ hybridization (FISH) method, and the jejunal AP activity was assayed histochemically. On day 40, the overfed rats in comparison with control animals displayed increased adiposity accompanied by enhanced AP activity, abundance of LAB, lower amounts of BAC and, thereafter, higher LAB/BAC ratio (L/B). The numbers of LAB and L/B index positively correlated with body fat, energy intake and AP activity, whereas numbers of BAC showed an opposite tendency. These results revealed the significance of nutritional imprint upon the post-weaning development of intestinal microbial and functional axis and contribute to better understanding of their involvement in energy-balance control and in adverse and/or positive regulation of adiposity.
- MeSH
- alkalická fosfatasa metabolismus MeSH
- Bacteroidetes izolace a purifikace klasifikace MeSH
- biodiverzita MeSH
- dieta MeSH
- financování organizované MeSH
- grampozitivní bakterie izolace a purifikace klasifikace MeSH
- histocytochemie MeSH
- hybridizace in situ fluorescenční MeSH
- jejunum enzymologie mikrobiologie MeSH
- krysa rodu rattus MeSH
- obezita mikrobiologie MeSH
- potkani Sprague-Dawley MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- srovnávací studie MeSH
