BACKGROUND: Osteoporosis (OP) has become a major public health issue, threatening the bone health of middle-aged and elderly people from all around the world. Changes in the gut microbiota (GM) are correlated with the maintenance of bone mass and bone quality. However, research results in this field remain highly controversial, and no systematic review or meta-analysis of the relationship between GM and OP has been conducted. This paper addresses this shortcoming, focusing on the difference in the GM abundance between OP patients and healthy controls based on previous 16S ribosomal RNA (rRNA) gene sequencing results, in order to provide new clinical reference information for future customized prevention and treatment options of OP. METHODS: According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), we comprehensively searched the databases of PubMed, Web of Science, Embase, Cochrane Library, and China National Knowledge Infrastructure (CNKI). In addition, we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis. We also implemented the Newcastle-Ottawa Scale (NOS), funnel plot analysis, sensitivity analysis, Egger's test, and Begg's test to assess the risk of bias. RESULTS: This research ultimately considered 12 studies, which included the fecal GM data of 2033 people (604 with OP and 1429 healthy controls). In the included research papers, it was observed that the relative abundance of Lactobacillus and Ruminococcus increased in the OP group, while the relative abundance for Bacteroides of Bacteroidetes increased (except for Ireland). Meanwhile, Firmicutes, Blautia, Alistipes, Megamonas, and Anaerostipes showed reduced relative abundance in Chinese studies. In the linear discriminant analysis Effect Size (LEfSe) analysis, certain bacteria showed statistically significant results consistently across different studies. CONCLUSIONS: This observational meta-analysis revealed that changes in the GM were correlated with OP, and variations in some advantageous GM might involve regional differences.
Middle Aged ; Aged ; Humans ; Gastrointestinal Microbiome/genetics* ; RNA, Ribosomal, 16S/genetics* ; Genes, rRNA ; Osteoporosis ; Feces

Ma-Mu-Ran Antidiarrheal Capsules (MMRAC) is traditional Chinese medicine that has been used to treat diarrhea caused by acute enteritis (AE) and bacillary dysentery in Xinjiang (China) for many years. However, the potential therapeutic mechanism of MMRAC for AE and its regulatory mechanism on host metabolism is unclear. This study used fecal metabolomics profiling with GC/MS and 16S rRNA gene sequencing analysis to explore the potential regulatory mechanisms of MMRAC on a dextran sulfate sodium salt (DSS)-induced mouse model of AE. Fecal metabolomics-based analyses were performed to detect the differentially expressed metabolites and metabolic pathways. The 16S rRNA gene sequencing analysis was used to assess the altered gut microbes at the genus level and for functional prediction. Moreover, Pearson correlation analysis was used to integrate differentially expressed metabolites and altered bacterial genera. The results revealed that six intestinal bacteria and seven metabolites mediated metabolic disorders (i.e., metabolism of amino acid, carbohydrate, cofactors and vitamins, and lipid) in AE mice. Besides, ten altered microbes mediated the differential expression of eight metabolites and regulated these metabolisms after MMRAC administration. Overall, these findings demonstrate that AE is associated with metabolic disorders and microbial dysbiosis. Further, we present that MMRAC exerts protective effects against AE by improving host metabolism through the intestinal flora.
Animals ; Antidiarrheals/pharmacology* ; Capsules ; Enteritis/genetics* ; Feces/microbiology* ; Genes, rRNA ; Metabolomics ; Mice ; RNA, Ribosomal, 16S/genetics*

Aims: Pyrodinium bahamense var. compressum is one of the principal causal agents of harmful algal blooms (HABs) in the coastal waters of Sabah, Malaysia. Seafood and aquaculture products tainted with lethal concentrations of the principal neurotoxin, saxitoxin, have been implicated in mortality and morbidity. The bacteria-algae association may play a key role in paralytic shellfish toxin (PST) production during a toxic bloom event. The production of PST during a harmful bloom is unclear and research on the bacterial diversity associated with Sabah P. bahamense is scarce. The present study examined the cultivable bacteria diversity associated with P. bahamense through 16S ribosomal RNA (rRNA) gene sequence analysis. Methodology and results: The V3-V4 region of the 16S rRNA gene sequence was amplified and used to identify bacterial populations associated with P. bahamense var. compressum. A total of 62 isolates were successfully isolated, belonging to three different phyla, which were Proteobacteria; 55 (89%), Bacteroidetes; 6 (10%) and Actinobacteria; 1 (1%). Out of 55 Proteobacteria, 27 isolates were gamma-Proteobacteria (Marinobacter salsuginis) and 28 of the isolates were alpha-Proteobacteria; Mameliella atlantica (13), Roseibium denhamense (10) and Roseibium hamelinense (5). The remaining bacteria isolates from the phyla Bacteroidetes and Actinobacteria were identified as Muricauda lutimaris (6) and Micrococcus luteus (1), respectively. Conclusion, significance and impact of study The analysis of the bacterial 16S rRNA gene revealed multiple bacterial taxa associated with the toxic P. bahamense var. compressum bloom. The findings of the present work will pave the way for further studies aimed at isolating and characterizing genes involved in the saxitoxin biosynthesis in the associated bacteria.
Bacteria--metabolism ; Genes, rRNA

OBJECTIVE: To explore the characteristics of mutations of four common pathogenic genes (GJB2, SLC26A4, GJB3 and 12S rRNA) among patients with nonsyndromic hearing loss (NSHL) from eastern Shandong. METHODS: Peripheral blood samples of 420 NSHL patients were collected, and a hereditary-deafness-gene microarray was used to detect GJB2 c.235delC, c.299-300delAT, c.35delG and c.176del16 mutations, GJB3 c.538C>T mutation, SLC26A4 c.2168A>G and c.IVS7-2A>G mutations, and 12S rRNA c.1555A>C and c.1494C>T mutations. For patients carrying single heterozygous mutations, the coding regions of the above genes were analyzed with Sanger sequencing. RESULTS: The results of the microarray assay and Sanger sequencing showed that 84 patients (20.00%) carried GJB2 mutations, with c.235delC (16.43%) and c.299-300delAT (7.86%) being most common. Seventy-five patients (17.86%) carried SLC26A4 mutations, for which c.IVS7-2A>G accounted for 15.71%. In addition, 5.95% of patients carried 12S rRNA mutations. Only one patient was found to carried GJB3 mutation (c.538C>T). CONCLUSION Common pathogenic mutations for NSHL in eastern Shandong included GJB2 c.235delC and SLC26A4 c.IVS7-2A>G. Of note, 5.95% of patients were due to 12S rRNA m.1555A>G mutation, which gave a frequency greater than other regions of China.
China ; Connexin 26 ; Connexins ; DNA Mutational Analysis ; DNA, Mitochondrial ; Deafness ; Genes, rRNA ; Hearing Loss ; Humans ; Mutation ; RNA, Ribosomal ; Sulfate Transporters

Cryptosporidium is a common intestinal protozoan that can lead to diarrhea in humans and dogs. The predominant species of infection are C. hominis and C. parvum in humans, and C. canis in dogs. However, C. canis can infect immunocompromised humans. Considering the close contact with humans, dogs have the potential to be reservoirs for human cryptosporidiosis. Breeding kennels are the major supply source of puppies for pet shops. The present study is to determine the molecular prevalence and characteristics of Cryptosporidium spp. found in breeding kennel dogs. A total of 314 fecal samples were collected from young and adult dogs kept in 5 breeding kennels. A polymerase chain reaction targeting the small subunit rRNA gene was employed for the detection of Cryptosporidium spp. To determine the species, the DNA sequences were compared to GenBank data. Overall, 21.0% of the fecal samples were positive for Cryptosporidium spp. infection. Cryptosporidium spp. was detected in all 5 facilities. A sequencing analysis demonstrated that all isolates shared 99–100% similarity with C. canis. The results suggest that Cryptosporidium spp. infection is present at a high-level in breeding kennel dogs. However, because dominant species in this survey was C. canis, the importance of breeding kennel dogs as reservoirs for Cryptosporidium spp. transmission to humans is likely to be low in Japan.
Adult ; Animals ; Base Sequence ; Breeding ; Cryptosporidiosis ; Cryptosporidium ; Databases, Nucleic Acid ; Diarrhea ; Dogs ; Genes, rRNA ; Humans ; Japan ; Polymerase Chain Reaction ; Prevalence

Facklamia hominis is a facultative anaerobic Gram-positive coccus generally displaying weak alpha-hemolysis and negativity for catalase and oxidase. Facklamia species are part of the normal flora of the female genitourinary tract and have been reported in invasive diseases such as meningitis and infective endocarditis, albeit rarely. A 67 year-old-man presented to hospital with a tender, erythematous epidermal cyst on the right side of his upper back. Simple excision of the cyst was performed and the pus was taken with a sterile swab for culture, yielding no growth. One week later, discharge was observed in the patient's wound site and a sterile swab for culture was taken. The colonies grown were identified as F. hominis by the Vitek 2 system (bioMérieux, France), and the result was then reported to clinicians, and later confirmed by 16S rRNA gene sequencing and matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry. To the best of our knowledge, this is the first reported case of F. hominis isolation from a clinical specimen in Korea.
Catalase ; Endocarditis ; Epidermal Cyst ; Female ; Genes, rRNA ; Humans ; Korea ; Mass Spectrometry ; Meningitis ; Oxidoreductases ; Suppuration ; Wounds and Injuries

BACKGROUND: Next-generation sequencing is increasingly used for taxonomic identification of pathogenic bacterial isolates. We evaluated the performance of a newly introduced whole genome-based bacterial identification system, TrueBac ID (ChunLab Inc., Seoul, Korea), using clinical isolates that were not identified by three matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems and 16S rRNA gene sequencing. METHODS: Thirty-six bacterial isolates were selected from a university-affiliated hospital and a commercial clinical laboratory. Species was identified by three MALDI-TOF MS systems: Bruker Biotyper MS (Bruker Daltonics, Billerica, MA, USA), VITEK MS (bioMérieux, Marcy l'Étoile, France), and ASTA MicroIDSys (ASTA Inc., Suwon, Korea). Whole genome sequencing was conducted using the Illumina MiSeq system (Illumina, San Diego, CA, USA), and genome-based identification was performed using the TrueBac ID cloud system (www.truebacid.com). RESULTS: TrueBac ID assigned 94% (34/36) of the isolates to known (N=25) or novel (N=4) species, genomospecies (N=3), or species group (N=2). The remaining two were identified at the genus level. CONCLUSIONS: TrueBac ID successfully identified the majority of isolates that MALDI-TOF MS failed to identify. Genome-based identification can be a useful tool in clinical laboratories, with its superior accuracy and database-driven operations.
Genes, rRNA ; Genome ; Gyeonggi-do ; Mass Spectrometry ; Seoul

In a population-based study with 4 years of follow up, we evaluated the prevalence of Coxiella burnetii in cattle on Ulleung Island, Korea. In this study, the rates of C. burnetii infection in cattle on Ulleung Island were determined by PCR and were found to be 0.3–1.0% in the period 2011–2014. All 17 C. burnetii partial 16S rRNA gene sequences from PCR-positive cattle were identical and 2 geographic representatives were included in our analysis. The nucleotide sequences of the 2 samples showed high (98.4–100%) identity with C. burnetii sequences obtained from the GenBank. In this long-term tracking study, the number of cattle positive for C. burnetii on Ulleung Island was low. To prevent the transmission of C. burnetii on Ulleung Island, control strategy should include biosecurity improvement in surveillance, livestock management, administering suitable tests before purchasing animals to detect C. burnetii shedders, and restricting movements between herds.
Animals ; Base Sequence ; Cattle ; Coxiella burnetii ; Coxiella ; Databases, Nucleic Acid ; Follow-Up Studies ; Genes, rRNA ; Korea ; Livestock ; Phylogeny ; Polymerase Chain Reaction ; Prevalence

The infection with Candida spp. for oral cavity is being increasingly reported. However, its variations have not yet been specifically described in periodontitis. The present study was conducted to use an uniplex 26S rRNA-based amplicons to detect and discriminate Candida using only one pair of ribosomal primers. A total of 50 patients with chronic periodontitis was involved in the study. Pure Candida colonies were isolated from 23 patients and genomic DNA was extracted, and PCR was conducted. Direct DNA sequencing followed by comprehensive phylogenetic analyses were performed to confirm the identity of Candida colonies. Results indicated that the ration of Candida-infected patients was 46%, with a high prevalence of C. albicans, followed by remarkably lower ratios of C. parapsilosis, C. glabrata, C. kefyr, and C. dubliniensis respectively. Phylogenetic analyses indicated obvious discrimination amongst the analyzed Candida species as each observed species occupied a distinctive phylogenetic position. The current results reported a simple, efficient, and low-cost detection of five species of Candida without the need for other costly techniques of molecular screening. The current findings may help dentists to easily take a snapshot of the patterns of Candida infection in periodontitis cases to assess the nature and grade of infection.
Candida ; Chronic Periodontitis ; Dentists ; Discrimination (Psychology) ; DNA ; Genes, rRNA ; Humans ; Mass Screening ; Mouth ; Periodontitis ; Polymerase Chain Reaction ; Prevalence ; RNA, Ribosomal ; Sequence Analysis, DNA

Iran bears a remarkable variety of reptiles. One of the lizard families occurring in Iran is the Family Agamidae which is widely are distributed throughout the old world. The large-scaled rock agamid, Laudakia nupta, is one of the well-known agamid. There are few reports of cloacal microbial on reptiles hence their function in cloacae remains unknown. Laudakia nupta usually live in rural and urban areas and close vicinity to man, they are likely to play an important role in the spread of disease that may be caused by these microorganisms and their transmission to man. Therefore, the aim of this study was to identify the bacterial flora colonizing the cloacal region of Laudakia nupta using molecular studies. The cloacal fluids were directly placed on nutrient agar (NA) plates and incubated at 25 ± 2 ℃ for 48 h. The resulting bacterial colonies were transferred to fresh nutrient agar (NA) plates for molecular studies. Twelve isolates were obtained from 17 specimens of Laudakia nupta. All bacteria isolates were identified as Bacillus subtillis (5), Bacillus cereus (4), Bacillus sp. (1), Pseudomonas putida (1), and Pseudomonas sp. (1) based on partial sequences of the 16 s rRNA gene. This is the first comprehensive report of bacteria spp. associated with cloaca of Laudakia nupta using molecular studies. In this research, we found that Laudakia nupta can be a carrier of bacteria which can transfer microorganisms to hosts.
Agar ; Bacillus ; Bacillus cereus ; Bacteria ; Cloaca ; Colon ; Genes, rRNA ; Humans ; Iran ; Lizards ; Pseudomonas ; Pseudomonas putida ; Reptiles