Rare Bacteria Research Articles

Diversity of rare and abundant bacteria in surface waters of the Southern Adriatic Sea

Bacteria are fundamental players in the functioning of the ocean, yet relatively little is known about the diversity of bacterioplankton assemblages and the factors shaping their spatial distribution. We investigated the diversity and community composition of bacterioplankton in surface waters of the Southern Adriatic sub-basin (SAd) in the Mediterranean Sea, across an environmental gradient from coastal to offshore stations. Bacterioplankton diversity was investigated using a whole-assemblage genetic fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA) coupled with 16S rDNA amplicon pyrosequencing. The main physico-chemical variables showed clear differences between coastal and offshore stations, with the latter displaying generally higher temperature, salinity and oxygen content. Bacterioplankton richness was higher in coastal than offshore waters. Bacterial community composition (BCC) differed significantly between coastal and offshore waters, and appeared to be influenced by temperature (explaining up to 30% of variance) and by the trophic state. Pyrosequencing evidenced dominance of Alphaproteobacteria (SAR11 cluster), uncultured Gammaproteobacteria (Rhodobacteraceae) and Cyanobacteria (Synechococcus). Members of the Bacteroidetes phylum were also abundant, and accounted for 25% in the station characterized by the higher organic carbon availability. Bacterioplankton assemblages included a few dominant taxa and a very large proportion (85%) of rare (<0.1%) bacteria, the vast majority of which was unique to each sampling station. The first detailed census of bacterioplankton taxa in the SAd sub-basin, performed using next generation sequencing, indicates that assemblages are highly heterogeneous, spatially structured according to the environmental conditions, and comprise a large number of rare taxa. The high turnover diversity, particularly evident at the level of the rare taxa, suggests to direct future investigations toward larger spatial or temporal scales, to better understand the role of bacterioplankton in the ecosystem functioning and the biogeochemistry of the basin.

Active and secreted IgA-coated bacterial fractions from the human gut reveal an under-represented microbiota core.

Host-associated microbiota varies in distribution depending on the body area inhabited. Gut microbes are known to interact with the human immune system, maintaining gut homoeostasis. Thus, we studied whether secreted-IgA (S-IgA) coat specific microbial taxa without inducing strong immune responses. To do so, we fractionated gut microbiota by flow cytometry. We found that active and S-IgA-coated bacterial fractions were characterized by a higher diversity than those observed in raw faecal suspensions. A long-tail effect was observed in family distribution, revealing that rare bacteria represent up to 20% of total diversity. While Firmicutes was the most abundant phylum, the majority of its sequences were not assigned at the genus level. Finally, the single-cell-based approach enabled us to focus on active and S-IgA-coated bacteria. Thus, we revealed a microbiota core common to the healthy volunteers participating in the study. Interestingly, this core was composed mainly of low frequency taxa (e.g. Sphingomonadaceae).

Sphingomonas Paucimobilis: An Unusual Cause of Meningitis—Case Report

Sphingomonas paucimobilis is an aerobic gram-negative bacillus. The bacteria can cause infections, which can be devastating and, therefore, the patients need adequate and early antibiotic cover. We are presenting an interesting case of meningitis secondary to an unusual S. paucimobilis infection. This is the second case to our knowledge in the literature on meningitis due to S. paucimobilis. The 31-year-old previously healthy man presented with 2 months' history of weight loss and loss of appetite. He had fever and headache for 3 weeks. He was also speaking irrelevantly for 3 weeks. He had change of behaviour for 1 day. The patient was a farmer and worked in the soil. On examination, he was not responding to questions and was not obeying commands. Computed tomography (CT) brain with contrast revealed meningeal enhancement and cerebral oedema. Lumbar puncture was performed. Cerebrospinal fluid (CSF) opening pressure was more than 50 cm H2O. CSF analysis showed meningitis picture with raised white cell count of 210/μL (predominantly neutrophils), glucose 3.1 mmol/L, and raised protein 2.47 g/L. He was given intravenous ceftriaxone. The following day, his condition deteriorated. CSF culture grew S. paucimobilis sensitive to ceftriaxone. S. paucimobilis causes severe meningitis. This can lead to hydrocephalus, which results in a need for extraventricular drainage. A good occupational history is important with regard to finding the aetiology of serious meningitis (including rare bacteria) even before the culture result is known. Appropriate treatment can be given early and adequately to prevent mortality.

Losing a Hip due to Inflamed Colon! Transient Self-limiting Colitis May Have Catastrophic Consequences

Introduction: Septic arthritis is a single organism infection. Typically, organisms seed the blood stream and infect susceptible joints. Rarely, more than one organism will affect one joint, and extremely rare colonic bacteria will be responsible for causing joint infections. I am presenting a case of a patient who lost her new hip because of a persistent infection from colonic bacteria. Case Description: This is a 61-year-old white female with hypercholesterolemia and bilateral hip osteoarthritis. She had a right total hip replacement in 2011. She presented with pain and limping, for which her old joint was found to be dislocated. She underwent a revision surgery, for which her hip was replaced and abnormal bone growth was removed. Her hospital stay was uneventful, and she was sent home after three days. She came back three weeks later with fever 102 F, sever night sweats, anorexia, and purulent discharge from her surgical site. She only reported two days of diarrhea two weeks earlier, with occasional bright red blood on top of her stool that was self-limited, and she never saught medical attention for it. The patient was taken to the operation room, she underwent debridement for her surgical site, and cultures from her wound grew Prevotella disiens and Enterococcus faecalis. Because of bacterial persistence and lack of healing, her artificial joint was removed and an antibiotic spacer was inserted. She underwent 16 debridement surgeries over the duration of two months. Multiple attempts failed to reveal the source of her infection, and a gastrointestinal malignancy was suspected. Diagnostic colonoscopy was done, which revealed scaring in the colon mucosa at the area of the splenic flexure. The entire remaining colon, including the distal terminal ileum, looked normal. Random colon biopsies did not reveal any active inflammation or architectural distortion. Mucosal atrophy and transmural fibrosis were seen in the affected scarred area. Discussion: Prosthetic joints are more prone to be infected than native joints. Bacterial seeding from blood stream is the most common cause of septic arthritis. A single type of organism is responsible for most of the joint infections. Literature reported remote infections secondary to colonic bacterial seeding, and is mostly related to colon malignancy. Review of literature failed to reveal a case of septic arthritis caused by two different organisms seeded from a transiently inflamed colonic mucosa. Physicians should pay a special attention to patients undergoing surgery to avoid a post surgical drop in blood pressure, which may end up in catastrophic consequences.

Analysis of oxygen reduction and microbial community of air-diffusion biocathode in microbial fuel cells

Microbes play irreplaceable role in oxygen reduction reaction of biocathode in microbial fuel cells (MFCs). In this study, air-diffusion biocathode MFCs were set up for accelerating oxygen reduction and microbial community analysis. Linear sweep voltammetry and Tafel curve confirmed the function of cathode biofilm to catalyze oxygen reduction. Microbial community analysis revealed higher diversity and richness of community in plankton than in biofilm. Proteobacteria was the shared predominant phylum in both biofilm and plankton (39.9% and 49.8%) followed by Planctomycetes (29.9%) and Bacteroidetes (13.3%) in biofilm, while Bacteroidetes (28.2%) in plankton. Minor fraction (534, 16.4%) of the total operational taxonomic units (3252) was overlapped demonstrating the disproportionation of bacterial distribution in biofilm and plankton. Pseudomonadales, Rhizobiales and Sphingobacteriales were exoelectrogenic orders in the present study. The research obtained deep insight of microbial community and provided more comprehensive information on uncultured rare bacteria.

Learning about rare bacteria

Learning about rare bacteria

Identification of Rare Pathogenic Bacteria in a Clinical Microbiology Laboratory: Impact of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

During the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.

Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count

Before 1990, the existence of heritable microbes in insects was recognized only by specialists working in the field of symbiosis. In the mid-1990s, the advent of simple PCR assays led to the widespread appreciation of one particular symbiont, Wolbachia. A deeper investigation of the biodiversity of symbionts led to a third phase of knowledge: bacteria from many different clades have evolved to be heritable symbionts, typically transmitted maternally and thought not to be routinely horizontally (infectiously) transmitted. In an issue of BMC Biology published in 2008, we observed that a diverse assemblage of maternally inherited bacteria were present in a broad range of arthropods [1]. Whilst Wolbachia remained the dominant bacterium, we noted that three other inherited bacteria, Spiroplasma, Cardinium and Arsenophonus, were also common. Overall, 33% of arthropod species examined were observed to carry at least one of these four symbionts. It is now clear that many more than one-third of species carry heritable symbionts. Any sampling regime produces 'false negatives', species that are infected but where infection is not detected. This occurs when infected individuals go unsampled, either because the symbiont is present in a minority of individuals in the population, or where the sample is from an uninfected population but individuals from other areas in the species range are infected. Further, surveys such as ours looked for particular bacteria, and ignored clades of bacteria that are restricted to particular host groups. Altogether, it is now clear that the majority of arthropod species carry inherited microbes, and that these microbes are diverse (Figure ​(Figure11). Figure 1 Evolutionary relationships of heritable bacteria found in arthropods (not exhaustive). Yellow, globally common heritable bacteria; green, rare heritable bacteria. In this piece we review two aspects of the biology of heritable symbionts where our views have changed substantially in the last five years. First, we note that the effect of infection on a host is more complex than previously considered. Symbionts increase host fitness more commonly than previously believed, and they may also have multiple impacts on their host. Second, whilst it has long been established that symbionts transfer from one host species to another, it was previously considered that these horizontal transfer events were rare. We now understand that some symbionts transfer very frequently between species. Further, symbiont genes transfer into the host nucleus, host genes transfer into the symbiont, and symbionts may also acquire genes from other symbionts. Thus, there are complex webs of genetic information exchange.

Post-traumatic endophthalmitis due to Brevibacterium casei: A case report

Endophthalmitis is a serious post-traumatic ocular complication that can lead to loss of vision. We report a case of acute post-traumatic endophthalmitis following a penetrating injury caused by an unusual organism, Brevibacterium casei . The patient was successfully treated with intravitreal antibiotics like ceftazidime and vancomycin, along with topical cefazolin and tobramycin. Brevibacterium casei can be added to the list of rare bacteria causing endophthalmitis and should be kept in mind by clinicians as a potential source of pathology.

Biased Diversity Metrics Revealed by Bacterial 16S Pyrotags Derived from Different Primer Sets

In recent years, PCR-based pyrosequencing of 16S rRNA genes has continuously increased our understanding of complex microbial communities in various environments of the Earth. However, there is always concern on the potential biases of diversity determination using different 16S rRNA gene primer sets and covered regions. Here, we first report how bacterial 16S rRNA gene pyrotags derived from a series of different primer sets resulted in the biased diversity metrics. In total, 14 types of pyrotags were obtained from two-end pyrosequencing of 7 amplicon pools generated by 7 primer sets paired by 1 of 4 forward primers (V1F, V3F, V5F, and V7F) and 1 of 4 reverse primers (V2R, V4R, V6R, and V9R), respectively. The results revealed that: i) the activated sludge exhibited a large bacterial diversity that represented a broad range of bacterial populations and served as a good sample in this methodology research; ii) diversity metrics highly depended on the selected primer sets and covered regions; iii) paired pyrotags obtained from two-end pyrosequencing of each short amplicon displayed different diversity metrics; iv) relative abundance analysis indicated the sequencing depth affected the determination of rare bacteria but not abundant bacteria; v) the primer set of V1F and V2R significantly underestimated the diversity of activated sludge; and vi) the primer set of V3F and V4R was highly recommended for future studies due to its advantages over other primer sets. All of these findings highlight the significance of this methodology research and offer a valuable reference for peer researchers working on microbial diversity determination.

Cure from the cave: volcanic cave actinomycetes and their potential in drug discovery

Volcanic caves have been little studied for their potential as sources of novel microbial species and bioactive compounds with new scaffolds. We present the first study of volcanic cave microbiology from Canada and suggest that this habitat has great potential for the isolation of novel bioactive substances. Sample locations were plot ted on a contour map that was compiled in ArcView 3.2. Over 400 bacterial isolates were obtained from the Helmcken Falls cave in Wells Gray Provincial Park, British Columbia. From our preliminary screen, of 400 isolates tested, 1% showed activity against extended spectrum ß-lactamase E. coli, 1.75% against Escherichia coli, 2.25% against Acinetobacter baumannii, and 26.50% against Klebsiella pneumoniae. In addition, 10.25% showed activity against Micrococcus luteus, 2% against methicillin resistant Staphylococcus aureus, 9.25% against Mycobacterium smegmatis, 6.25% Pseudomonas aeruginosa and 7.5% against Candida albicans. Chemical and physical characteristics of three rock wall samples were studied using scanning electron microscopy and f lame atomic absorption spectrometry. Calcium (Ca), iron (Fe), and aluminum (Al) were the most abundant components while magnesium (Mg), sodium (Na), arsenic (As), lead (Pb), chromium (Cr), and barium (Ba) were second most abundant with cadmium (Cd) and potassium (K) were the least abundant in our samples. Scanning electron microscopy (SEM) showed the presence of microscopic life forms in all three rock wall samples. 16S rRNA gene sequencing of 82 isolates revealed that 65 (79.3%) of the strains belong to the Streptomyces genus and 5 (6.1%) were members of Bacillus, Pseudomonas, Nocardia and Erwinia genera. Interestingly, twelve (14.6%) of the 16S rRNA sequences showed similarity to unidentified ribosomal RNA sequences in the library databases, the sequences of these isolates need to be further investigated using the EzTaxon-e database (http://eztaxon-e. ezbiocloud.net/) to determine whether or not these are novel species. Nevertheless, this suggests the possibility that they could be unstudied or rare bacteria. The Helmcken Falls cave microbiome possesses a great diversity of microbes with the potential for studies of novel microbial interactions and the isolation of new types of antimicrobial agents.

Advantages and Limitations of Ribosomal RNA PCR and DNA Sequenc-ing for Identification of Bacteria in Cardiac Valves of Danish Patients

Studies on the value of culture-independent molecular identification of bacteria in cardiac valves are mostly restricted to comparing agreement of identification to what is obtained by culture to the number of identified bacteria in culture-negative cases. However, evaluation of the usefulness of direct molecular identification should also address weaknesses, their relevance in the given setting, and possible improvements.In this study cardiac valves from 56 Danish patients referred for surgery for infective endocarditis were analysed by microscopy and culture as well as by PCR targeting part of the bacterial 16S rRNA gene followed by DNA sequencing of the PCR product. PCR and DNA sequencing identified significant bacteria in 49 samples from 43 patients, including five out of 13 culture-negative cases. No rare, exotic, or intracellular bacteria were identified. There was a general agreement between bacterial identity obtained by ribosomal PCR and DNA sequencing from the valves and bacterial isolates from blood culture. However, DNA sequencing of the 16S rRNA gene did not discriminate well among non-haemolytic streptococci, especially within the Streptococcus mitis group.Ribosomal PCR with subsequent DNA sequencing is an efficient and reliable method of identifying the cause of IE, but exact species identification of some of the most common causes, i.e. non-haemolytic streptococci, may be improved with other molecular methods.

全身性破傷風患者の創傷部から分離した &lt;i&gt;Clostridium tetani&lt;/i&gt; の 1 症例

Clostridium tetani is widely distributed in ground or mud, especially in field and pond-shore surface layers. C. tetani is rarely isolated from specimens of patients with tetanus, and is generally diagnosed based on clinical symptoms such as trismus or general tonic spasms. This means that positive C. tetani infection is rarely diagnosed bacterially. Using gram straing, we identified C. tetani in specimens from patients suspected of C. tetani infection brought to the Kitasato University Hospital emergency center. Rapid gram staining information in the bacteriology laboratory is expected to improve recovery from C. tetani infection. It is therefore necessary to ensure clinical specimen quality control, and to keep standard strains of rare bacteria for isolation and identification.

Manifestations vasculaires des infections àCampylobacter fetus subsp. fetus : à propos de deux cas

IntroductionCampylobacter fetus is a rare Gram-negative bacteria affecting especially elderly and immunocompromised patients, and that is responsible of vascular and cutaneous involvement. ObservationsWe report two cases of C. fetus infection in two diabetic male patients, aged 75 and 85years. The first patient was admitted for chronic fever. First-line examinations were inconclusive. Combined positron emission tomography and computed imaging tomography (PET-CT) diagnosed an infection of a previously operated popliteal aneurysm. The patient underwent surgery, and per-operative samples were positive for C. fetus. The second patient was admitted for a leg cellulitis. Blood cultures were positive for C. fetus. PET-CT found a septic superficial thrombophlebitis. The outcome was favorable for both patients with prolonged antibiotic therapy. ConclusionVascular involvement should be suspected in the presence of C. fetus infections. PET-CT may be useful, as other imaging modalities are not always contributive.

Changes in Bacterial Community Structure after Exposure to Silver Nanoparticles in Natural Waters

Silver nanoparticles (AgNPs) are widely used in commercial products as antibacterial agents, but AgNPs might be hazardous to the environment and natural aquatic bacterial communities. Our recent research demonstrated that AgNPs rapidly but temporarily inhibited natural bacterioplankton production. The current study investigates the mechanism for the observed bacterial reaction to AgNPs by examining how AgNPs impact bacterial abundance, metabolic activity (5-cyano-2,3-ditolyl tetrazolium chloride (CTC+) cells), and 16S rRNA community composition. Natural bacterioplankton communities were dosed with carboxy-functionalized AgNPs at four concentrations (0.01-1 mg-Ag/L), incubated in triplicate, and monitored over 5 days. Ionic silver (AgNO(3)) and Milli-Q water treatments were used as a positive and negative control, respectively. Four general AgNP exposure responses, relative to the negative control, were observed: (1) intolerant, (2) impacted but recovering, (3) tolerant, and (4) stimulated phylotypes. Relationships between cell activity indicators and bacterial phylotypes, suggested that tolerant and recovering bacteria contributed the most to the community's productivity and rare bacteria phylotypes stimulated by AgNPs did not appear to contribute much to cell activity. Overall, natural bacterial communities tolerated single, low level AgNP doses and had similar activity levels to the negative control within five days of exposure, but bacterial community composition was different from that of the control.

Graft-versus-host disease disrupts intestinal microbial ecology by inhibiting Paneth cell production of α-defensins

AbstractAllogeneic hematopoietic stem cell transplantation (SCT) is a curative therapy for various hematologic disorders. Graft-versus-host disease (GVHD) and infections are the major complications of SCT, and their close relationship has been suggested. In this study, we evaluated a link between 2 complications in mouse models. The intestinal microbial communities are actively regulated by Paneth cells through their secretion of antimicrobial peptides, α-defensins. We discovered that Paneth cells are targeted by GVHD, resulting in marked reduction in the expression of α-defensins, which selectively kill noncommensals, while preserving commensals. Molecular profiling of intestinal microbial communities showed loss of physiologic diversity among the microflora and the overwhelming expansion of otherwise rare bacteria Escherichia coli, which caused septicemia. These changes occurred only in mice with GVHD, independently on conditioning-induced intestinal injury, and there was a significant correlation between alteration in the intestinal microbiota and GVHD severity. Oral administration of polymyxin B inhibited outgrowth of E coli and ameliorated GVHD. These results reveal the novel mechanism responsible for shift in the gut flora from commensals toward the widespread prevalence of pathogens and the previously unrecognized association between GVHD and infection after allogeneic SCT.

Specific Sorting of Single Bacterial Cells with Microfabricated Fluorescence-Activated Cell Sorting and Tyramide Signal Amplification Fluorescence in Situ Hybridization

When attempting to probe the genetic makeup of diverse bacterial communities that elude cell culturing, researchers face two primary challenges: isolation of rare bacteria from microbial samples and removal of contaminating cell-free DNA. We report a compact, low-cost, and high-performance microfabricated fluorescence-activated cell sorting (μFACS) technology in combination with a tyramide signal amplification fluorescence in situ hybridization (TSA-FISH) to address these two challenges. The TSA-FISH protocol that was adapted for flow cytometry yields a 10-30-fold enhancement in fluorescence intensity over standard FISH methods. The μFACS technology, capable of enhancing its sensitivity by ~18 dB through signal processing, was able to enrich TSA-FISH-labeled E. coli cells by 223-fold. The μFACS technology was also used to remove contaminating cell-free DNA. After two rounds of sorting on E. coli mixed with λ-phage DNA (10 ng/μL), we demonstrated over 100,000-fold reduction in λ-DNA concentration. The integrated μFACS and TSA-FISH technologies provide a highly effective and low-cost solution for research on the genomic complexity of bacteria as well as single-cell genomic analysis of other sample types.

Complete Genome Sequence of Streptomyces cattleya NRRL 8057, a Producer of Antibiotics and Fluorometabolites

Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of the rare bacteria known to synthesize fluorinated metabolites. The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons.

Activity of abundant and rare bacteria in a coastal ocean

The surface layer of the oceans and other aquatic environments contains many bacteria that range in activity, from dormant cells to those with high rates of metabolism. However, little experimental evidence exists about the activity of specific bacterial taxa, especially rare ones. Here we explore the relationship between abundance and activity by documenting changes in abundance over time and by examining the ratio of 16S rRNA to rRNA genes (rDNA) of individual bacterial taxa. The V1-V2 region of 16S rRNA and rDNA was analyzed by tag pyrosequencing in a 3-y study of surface waters off the Delaware coast. Over half of the bacterial taxa actively cycled between abundant and rare, whereas about 12% always remained rare and potentially inactive. There was a significant correlation between the relative abundance of 16S rRNA and the relative abundance of 16S rDNA for most individual taxa. However, 16S rRNA:rDNA ratios were significantly higher in about 20% of the taxa when they were rare than when abundant. Relationships between 16S rRNA and rDNA frequencies were confirmed for five taxa by quantitative PCR. Our findings suggest that though abundance follows activity in the majority of the taxa, a significant portion of the rare community is active, with growth rates that decrease as abundance increases.

Molecular diversity of bacteria in Yunnan yellow cattle (Bos taurs) from Nujiang region, China

The rumen content of four Yunnan Yellow Cattle (Bos taurs) were collected to determine the bacteria diversity by using 16S rRNA gene sequence analysis. A total of 129 sequences were examined and the sequences were referred as 107 OTU (Operational Taxonomy Unit) according to the similarity level of 97% in gene sequence. Similarity analysis revealed that Yunnan Yellow Cattle had 12 sequences (10 OTU) shared 97% or greater similarity with cultured rumen bacteria Butyrivibrio fibrisolvens, Succiniclasticum ruminis, Ruminococcus bromii, Clostridium proteoclasticum, Ruminococcus flavefaciens, Pseudobutyrivibrio ruminis, Jeotgalicoccus psychrophilus, and Prevotella ruminicola, which accounting for 9.3% of the total clones (9.2% of the total OTU). The further 12 sequences (9 OTU) shared 90-97% similarity with cultured bacteria Clostridium aminobutyricum, butyrate-producing bacterium, Schwartzia succinivorans, Prevotella ruminicola, Eubacterium ruminantium, Ruminococcus albus, and Clostridium termitidis, also accounting for 9.3% of the total sequences (8.3% of the total OTU). The remaining 105 sequences (90 OTU) shared less than 90% similarity with cultured bacteria, accounting for 81.4% of the total sequences (82.5% of the total OTU). According to the phylogenetic analysis, all sequences were phylogenetically placed within phyla of low G+C subdivision (accounting for 72.1 and 72.5% of the total clones and OTU, respectively) and CFB subdivision (Cytophaga-Flexibacter-Bacteroides; accounting for 27.9 and 27.5% of the total clones and OTU, respectively). Among the examined clones, rare bacteria Jeotgalicoccus psychrophilus was detected in the rumen of cattle.