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F1000Research 2021: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains...
: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized. We sought to conduct metagenomic sequencing on cases of ocular and periocular sarcoidosis, none of them with previously identified infectious causes. : Archival tissue specimens of 16 subjects with biopsies of ocular and periocular tissues that were positive for non-caseating granulomas were used as cases. Four archival tissue specimens that did not demonstrate non-caseating granulomas were also included as controls. Genomic DNA was extracted from tissue sections. DNA libraries were generated from the extracted genomic DNA and the libraries underwent next-generation sequencing. : We generated between 4.8 and 20.7 million reads for each of the 16 cases plus four control samples. For eight of the cases, we identified microbial pathogens that were present well above the background, with one potential pathogen identified for seven of the cases and two possible pathogens for one of the cases. Five of the eight cases were associated with bacteria ( and ), two cases with fungi ( ) and one case with a virus (Mupapillomavirus 1). Interestingly, four of the five bacterial species are also part of the human oral microbiome. : Using a metagenomic sequencing we identified possible infectious causes in half of the ocular and periocular sarcoidosis cases analyzed. Our findings support the proposition that sarcoidosis could be an etiologically heterogenous disease. Because these are previously banked samples, direct follow-up in the respective patients is impossible, but these results suggest that sequencing may be a valuable tool in better understanding the etiopathogenesis of sarcoidosis and in diagnosing and treating this disease.
Topics: Bacteria; High-Throughput Nucleotide Sequencing; Humans; Metagenome; Metagenomics; Microbiota; Sarcoidosis
PubMed: 36212901
DOI: 10.12688/f1000research.55090.1 -
Microorganisms Oct 2020Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic...
Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., and ). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.
PubMed: 33023015
DOI: 10.3390/microorganisms8101522 -
Frontiers in Physiology 2021New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However,...
Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream () Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization.
New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal and was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of associated with the presence of . The intestinal gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and ) and metal-reducing ( and ) bacteria. Other inflammatory markers (α) were up-regulated in PAP fish, positively correlating the intestinal gene with the inflammasome activator , whereas the systemic expression of and α was negatively correlated with the Bacilli class in PAP fish and positively correlated with in non-PAP fish. Overall changes in the expression pattern of , galectins (), and toll-like receptors () reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of - and -mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.
PubMed: 34675821
DOI: 10.3389/fphys.2021.748265 -
Medicine May 2008The etiologic evaluation of uveitis is frequently unsuccessful when noninvasive methods are used. We conducted a prospective study to evaluate systematic screening for...
The etiologic evaluation of uveitis is frequently unsuccessful when noninvasive methods are used. We conducted a prospective study to evaluate systematic screening for pathogens of uveitis. All patients with uveitis referred to the participating tertiary ophthalmology departments from January 2001 to September 2007 underwent intraocular and serum specimen collection. The standardized protocol for laboratory investigations included universal polymerase chain reaction (PCR)-based detection of any bacteria and mycoses, specific PCR-based detection of fastidious (difficult-to-grow) bacteria and herpes viruses, and culture of vitreous fluid. Sera were tested for fastidious bacteria. Among the 1321 included patients (1520 specimens), infection was diagnosed in 147 (11.1%) patients: 78 (53%) were caused by fastidious bacteria that included spirochetes, Bartonella species, intracellular bacteria (Chlamydia species, Rickettsia species, Coxiella burnetii), and Tropheryma whipplei; 18 by herpes viruses; and 9 by fungi. Bartonella quintana, Coxiella burnetii, Paracoccus yeei, Aspergillus oryzae, and Cryptococcus albidus were found to be associated with uveitis for the first time, to our knowledge. We recommend applying a 1-step diagnostic procedure that incorporates intraocular, specific microbial PCR with serum analyses in tertiary centers to determine the etiology of uveitis.
Topics: Adult; Aged; Aged, 80 and over; Bacteria; Child, Preschool; Eye Infections, Bacterial; Female; Humans; Male; Middle Aged; Polymerase Chain Reaction; Serologic Tests; Tropheryma; Uveitis
PubMed: 18520326
DOI: 10.1097/MD.0b013e31817b0747 -
Laboratory Animals Oct 2014Correct identification of bacteria is crucial for the management of rodent colonies. Some bacteria are difficult to identify phenotypically outside reference...
Correct identification of bacteria is crucial for the management of rodent colonies. Some bacteria are difficult to identify phenotypically outside reference laboratories. In this study, we evaluated the utility of 16S ribosomal DNA (rDNA) sequencing as a means of identifying a collection of 30 isolates of rodent origin which are conventionally difficult to identify. Sequence analysis of the first approximate 720 to 880 bp of the 5'- end of 16S rDNA identified 25 isolates (83.33%) with ≥ 99% similarity to a sequence of a type strain, whereas three isolates (10%) displayed a sequence similarity ≥ 97% but <99% to the type strain sequences. These similarity scores were used to define identification to species and genus levels, respectively. Two of the 30 isolates (6.67%) displayed a sequence similarity of ≥ 95 but <97% to the reference strains and were thus allocated to a family. This technique allowed us to document the association of mice with bacteria relevant for the colonies management such as Pasteurellaceae, Bordetella hinzii or Streptococcus danieliae. In addition, human potential pathogens such as Acinetobacter spp., Ochrobactrum anthropi and Paracoccus yeei or others not yet reported in mouse bacterial species such as Leucobacter chironomi, Neisseria perflava and Pantoea dispersa were observed. In conclusion, the sequence analysis of 16S rDNA proved to be a useful diagnostic tool, with higher performance characteristics than the classical phenotypic methods, for identification of laboratory animal bacteria. For the first time this method allowed us to document the association of certain bacterial species with the laboratory mouse.
Topics: Animal Husbandry; Animals; Animals, Laboratory; Bacteria; Mice; Molecular Sequence Data; RNA, Ribosomal, 16S; Rats; Sequence Analysis, DNA
PubMed: 24876090
DOI: 10.1177/0023677214538240 -
Journal of Global Infectious Diseases Apr 2011Purine compounds are special types of alkaloids. Caffeine and aminophylline are considered the most important members of purines due to their wide use in therapeutics.
BACKGROUND
Purine compounds are special types of alkaloids. Caffeine and aminophylline are considered the most important members of purines due to their wide use in therapeutics.
AIMS
To detect any potential antibacterial effects on pathogenic bacteria of the widely prescribed members of purines caffeine and aminophylline.
MATERIALS AND METHODS
Two species of gram-positive bacteria and five species of gram-negative bacteria were exposed to these purine agents. Antibacterial effects of the tested purines were determined using the spectrophotometer method to assess the minimum inhibition concentrations (MIC).
RESULTS
Among the strains of bacteria tested, Bacillus subtilis showed the most susceptibility to purine agents. Staphylococcus aureus and Bacillus subtilis were found to be more susceptible to caffeine than the other strains. Aminophylline showed inhibitory action on many isolates, especially at the concentration of 10mg/ml. Paracoccus yeei demonstrated resistance to all tested purine compounds up to a concentration of 10.5mg/ml.
CONCLUSIONS
Caffeine and aminophylline had the ability to inhibit many strains of pathogenic bacteria.
PubMed: 21731299
DOI: 10.4103/0974-777X.81689