Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism

Although a few studies have described the microbiome composition of TB sputa based on 16S ribosomal DNA, these studies did not compare to non-TB samples and the nature of the method does not allow any functional inference. This is the first study to apply such technology using clinical specimens and obtained functional transcriptional data on all three aspects simultaneously.

A Two-Step PCR Protocol Enabling Flexible Primer Choice and High Sequencing Yield for Illumina MiSeq Meta-Barcoding

High-throughput amplicon sequencing that primarily targets the 16S ribosomal DNA (rDNA) (for bacteria and archaea) and the Internal Transcribed Spacer rDNA (for fungi) have facilitated microbial community discovery across diverse environments. A three-step PCR that utilizes flexible primer choices to construct the library for Illumina amplicon sequencing has been applied to several studies in forest and agricultural systems. The three-step PCR protocol, while producing high-quality reads, often yields a large number (up to 46%) of reads that are unable to be assigned to a specific sample according to its barcode. Here, we improve this technique through an optimized two-step PCR protocol. We tested and compared the improved two-step PCR meta-barcoding protocol against the three-step PCR protocol using four different primer pairs (fungal ITS: ITS1F-ITS2 and ITS1F-ITS4, and bacterial 16S: 515F-806R and 341F-806R). We demonstrate that the sequence quantity and recovery rate were significantly improved with the two-step PCR approach (fourfold more read counts per sample; determined reads ≈90% per run) while retaining high read quality (Q30 > 80%). Given that synthetic barcodes are incorporated independently from any specific primers, this two-step PCR protocol can be broadly adapted to different genomic regions and organisms of scientific interest.

Exploration of Crucial Mediators for Carotid Atherosclerosis Pathogenesis Through Integration of Microbiome, Metabolome, and Transcriptome

BackgroundCarotid atherosclerosis (CAS) is an important cause of stroke. Although interactions between the gut microbiome and metabolome have been widely investigated with respect to the pathogenesis of cardiovascular diseases, information regarding CAS remains limited.Materials and MethodsWe utilized 16S ribosomal DNA sequencing and untargeted metabolomics to investigate the alterations in the gut microbiota and plasma metabolites of 32 CAS patients and 32 healthy controls. The compositions of the gut microbiota differed significantly between the two groups, and a total of 11 differentially enriched genera were identified. In the metabolomic analysis, 11 and 12 significantly changed metabolites were screened in positive (POS) and negative (NEG) modes, respectively. α-N-Phenylacetyl-L-glutamine was an upregulated metabolite in CAS patients detected in both POS and NEG modes and had the highest | log2(fold change)| in POS mode. In addition, transcriptomic analysis was performed using the GSE43292 dataset.ResultsA total of 132 differentially expressed genes (DEGs) were screened. Among the upregulated DEGs in CAS patients, FABP4 exhibited the highest | log2(fold change)|. Furthermore, FABP4 was positively associated with Acidaminococcus and had the highest Spearman’s correlation coefficient and the most significant p-value among the microbiota–DEG pairs.ConclusionIn this study, we investigated the potential “microbiota–metabolite–gene” regulatory axis that may act on CAS, and our results may help to establish a theoretical basis for further specialized study of this disease.

Capnocytophaga canimorsus Meningitis – Diagnosis with 16S rDNA PCR when Conventional Methods Failed to Identify the Causative Agent

Meningitis whether bacterial or viral, poses many challenges to clinicians as the causative agent is often not found. According to guidelines, it is standard to start empiric treatment before a Cerebrospinal Fluid (CSF) sample is obtained. Meningitis, if not diagnosed and treated early, can lead to high morbidity and mortality rates with serious neurological sequelae. While the most common cases of bacterial meningitis are related to Streptococcus pneumoniae and Neisseria meningitidis, this clinical case report found a rare case of meningitis caused by a zoonotic pathogen, Capnocytophaga canimorsus; a commensal found as part of the normal flora of dogs and cats. This rare organism was identified with the help of broad range 16S ribosomal DNA Polymerase Chain Reaction (rDNA PCR), an emerging technique that is now increasingly useful in rapid diagnosis especially if the offending agent is not timely identified and conventional methods have failed, making diagnosis and management difficult for physicians.

The influence of starter cultures on the lactic acid bacteria microbiota of Petrovac sausage

Petrovac sausage (Petrovská klobása) is a high-quality fermented dry sausage produced traditionally in the municipality of Ba?ki Petrovac (Vojvodina, Serbia). The product is characterised by specific and recognised texture, aroma and colour, produced without additives or preservatives. Lactic acid bacteria (LAB) microbiota plays an important role in production of the sausage. The aim of the paper is to monitor the changes in LAB during the production of Petrovac sausage. Samples of sausages were prepared without and with the addition of starter culture Staphylococcus xylosus as well as combined starter culture Lactiplantibacillus plantarum and S. xylosus, and produced at two different temperature ranges. A total number of 495 strains were isolated from 33 samples of Petrovac sausage during 120 days of production process. Characterisation of the isolates was performed by phenotypic tests, while molecular identification of the representative strains was done by 16S ribosomal DNA sequencing. The total number of LAB was about 8 log (Colony Forming Unit (CFU))/g in all samples, while the number of staphylococci was about 4 log CFU/g. Molecular identification confirmed that all isolates belonged to the following species: Levilactobacillus brevis, Leuconostoc mesenteroides, Lactiplantibacillus plantarum and Pediococcus pentosaceus. Lactobacilli and Leuconostoc spp. dominate the total LAB strains, while P. pentosaceus was isolated at the lowest frequency.

Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19

BackgroundSARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient’s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group.ResultsStatistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms.ConclusionOur study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.

Impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study

Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). Conclusion In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments.