Rabbit microbiota across the whole body revealed by 16S rRNA gene amplicon sequencing

Background Rabbit can produce meat, fur and leather, and serves as an important biomedical animal model. Understanding the microbial community of rabbits helps to raise rabbits healthily and better support their application as animal models. Results In this study, we selected 4 healthy Belgium gray rabbits to collect the microbial samples from 12 body sites, including skin, lung, uterus, mouth, stomach, duodenum, ileum, jejunum, colon, cecum, cecal appendix and rectum. The microbiota across rabbit whole body was investigated via 16S rRNA gene amplicon sequencing. After quality control, 46 samples were retained, and 3,148 qualified ASVs were obtained, representing 23 phyla and 264 genera. Based on the weighted UniFrac distances, these samples were divided into the large intestine (Lin), stomach and small intestine (SSin), uterus (Uter), and skin, mouth and lung (SML) groups. The diversity of Lin microbiota was the highest, followed by those of the SSin, Uter and SML groups. In the whole body, Firmicutes (62.37%), Proteobacteria (13.44%) and Bacteroidota (11.84%) were the most predominant phyla. The relative abundance of Firmicutes in the intestinal tract was significantly higher than that in the non-intestinal site, while Proteobacteria was significantly higher in the non-intestinal site. Among the 264 genera, 35 were the core microbiota distributed in all body sites. Sixty-one genera were specific in the SML group, while 13, 8 and 1 were specifically found in the Lin, SSin and Uter groups, respectively. The Lin group had the most difference with other groups, there were average 72 differential genera between the Lin and other groups. The functional prediction analysis showed that microbial function within each group was similar, but there was a big difference between the intestinal tracts and the non-intestinal group. Notably, the function of microorganism in uterus and mouth were the most different from those in the gastrointestinal sites; rabbit’s coprophagy of consuming soft feces possibly resulted in little differences of microbial function between stomach and large intestinal sites. Conclusion Our findings improve the knowledge about rabbit microbial communities throughout whole body and give insights into the relationship of microbial communities among different body sites in health rabbits.

Comparison of swab types for collection and analysis of microorganisms

The human microbiome has begun to emerge as a potential forensic tool, with varied applications ranging from unique identification to investigative leads that link individuals and/or locations. The relative abundance of the combined DNA of the microbiome, compared to human nuclear DNA, may expand potential sources of biological evidence, especially in cases with transfer or low-copy number DNA samples. This work sought to determine the optimal swab type for the collection and analysis of the microbiome. A bacterium (Proteus mirabilis) was deposited by pipette onto four swab types (cotton, flocked, dental applicators, and dissolvable), and extraction and real-time PCR quantitation of the bacterial DNA were performed, which allowed for absolute microbial DNA recovery and comparison of yields across the four sampling substrates. Flocked swabs had the highest yield (~1240 ng) compared to the cotton swabs (~184 ng), dental applicators (~533 ng), and dissolvable swabs (~430 ng). The collection efficiency was further evaluated for cotton and flocked swabs using dried microbial samples spotted onto non-porous surfaces (treated wood, glass, plastic, and tile). Flocked swabs performed consistently better across wood, glass, and tile, but showed decreased recovery from plastic. The cotton swabs failed in the recovery of P. mirabilis DNA across all surfaces. Knowing the appropriate sampling substrate will be useful as others continue to investigate the use of the microbiome as a forensics tool.

Translocation of vaginal microbiota is involved in impairment and protection of uterine health

The vaginal and uterine microbiota play important roles in the health of the female reproductive system. However, the interactions among the microbes in these two niches and their effects on uterine health remain unclear. Here we profile the vaginal and uterine microbial samples of 145 women, and combine with deep mining of public data and animal experiments to characterize the microbial translocation in the female reproductive tract and its role in modulating uterine health. Synchronous variation and increasing convergence of the uterine and vaginal microbiome with advancing age are shown. We also find that transplanting certain strains of vaginal bacteria into the vagina of rats induces or reduces endometritis-like symptoms, and verify the damaging or protective effects of certain vaginal bacteria on endometrium. This study clarifies the interdependent relationship of vaginal bacterial translocation with uterine microecology and endometrial health, which will undoubtedly increase our understanding of female reproductive health.

Development and validation of a novel customized medium for the marine microbial culture

Marine microbes are difficult to culture and hence it takes expensive measure to study. Mostly metagenomics are suggested for marine microbial characterization instead of culturing them in a suitable medium. In this study, a new approach has been developed to culture the marine microorganisms. We customized the LB agar and liquid medium by adjusting the pH and salt concentration at seawater level and then studied the microbial load, their growth rate by turbidity assay and also identified their morphology through gram staining. This study ensures the comfortable growth of marine microbes at the laboratory level, which would further help the marine biotechnologists and microbiologists to work smoothly with marine microbial samples. Bioresearch Commu. 7(2): 999-1003, 2021 (June)

Screening for Methane Utilizing Mixed Communities with High Polyhydroxybutyrate (PHB) Production Capacity Using Different Design Approaches

With the adverse environmental ramifications of the use of petroleum-based plastic outweighing the challenges facing the industrialization of bioplastics, polyhydroxyalkanoate (PHA) biopolymer has gained broad interest in recent years. Thus, an efficient approach for maximizing polyhydroxybutyrate (PHB) polymer production in methanotrophic bacteria has been developed using the methane gas produced in the anaerobic digestion process in wastewater treatment plants (WWTPS) as a carbon substrate and an electron donor. A comparison study was conducted between two experimental setups using two different recycling strategies, namely new and conventional setups. The former setup aims to recycle PHB producers into the system after the PHB accumulation phase, while the latter recycles the biomass back into the system after the exponential phase of growth or the growth phase. The goal of this study was to compare both setups in terms of PHB production and other operational parameters such as growth rate, methane uptake rate, and biomass yield using two different nitrogen sources, namely nitrate and ammonia. The newly proposed setup is aimed at stimulating PHB accumulating type II methanotroph growth whilst enabling other PHB accumulators to grow simultaneously. The success of the proposed method was confirmed as it achieved highest recorded PHB accumulation percentages for a mixed culture community in both ammonia- and nitrate-enriched media of 59.4% and 54.3%, respectively, compared to 37.8% and 9.1% for the conventional setup. Finally, the sequencing of microbial samples showed a significant increase in the abundance of type II methanotrophs along with other PHB producers, confirming the success of the newly proposed technique in screening for PHB producers and achieving higher PHB accumulation.

Bacteremic sepsis leads to higher mortality when adjusting for confounders with propensity score matching

One can falsely assume that it is well known that bacteremia is associated with higher mortality in sepsis. Only a handful of studies specifically focus on the comparison of culture-negative and culture-positive sepsis with different conclusions depending on study design. The aim of this study was to describe outcome for critically ill patients with either culture-positive or -negative sepsis in a clinical review. We also aimed to identify subphenotypes of sepsis with culture status included as candidate clinical variables. Out of 784 patients treated in intensive care with a sepsis diagnosis, blood cultures were missing in 140 excluded patients and 95 excluded patients did not fulfill a sepsis diagnosis. Of 549 included patients, 295 (54%) had bacteremia, 90 (16%) were non-bacteremic but with relevant pathogens detected and in 164 (30%) no relevant pathogen was detected. After adjusting for confounders, 90-day mortality was higher in bacteremic patients, 47%, than in non-bacteremic patients, 36%, p = 0.04. We identified 8 subphenotypes, with different mortality rates, where pathogen detection in microbial samples were important for subphenotype distinction and outcome. In conclusion, bacteremic patients had higher mortality than their non-bacteremic counter-parts and bacteremia is more common in sepsis when studied in a clinical review. For reducing population heterogeneity and improve the outcome of trials and treatment for sepsis, distinction of subphenotypes might be useful and pathogen detection an important factor.

A Full-Ocean-Depth Sampler for Hadal Microbes Based on Multistage Membrane Filters With In-Situ Preservation

In order to obtain high-quality microbial samples from the hadal zone, which has a depth of over 6,000 m, a full-ocean-depth sampler with the function of in-situ filtration and preservation was developed. A flow pump and several membrane filters were used for in-situ filtration under the sea. With a multistage filtering structure, the microbes can be initially screened according to their sizes. To avoid the degradation of microbial ribonucleic acid (RNA), a special structure was designed to inject the RNAlater solution into the samples immediately after the filtration. The sampler was tested in our laboratory and deployed during Mariana TS-15 in 2019. It was installed on a hadal lander of Shanghai Ocean University and deployed at MBR02 (11.371°N, 142.587°E, 10,931 m) in the Mariana Trench. A total of 20 L of in-situ seawater was filtered, and membranes with pore sizes of 3 and 0.2 μm were preserved. The study is expected to provide important support for the establishment of a hadal microbial gene pool.

Reduction in Enteroccocus faecalis counts produced by three file systems in severely curved canals

Aim: This study evaluated the effectiveness of the mechanical reduction of intracanal bacteria produced by the endodontic systems Reciproc Blue (VDW GmbH), XP-Endo Shaper (FKG Dentaire) and ProTaper Next (Dentsply Sirona Endodontics) in severely curved canals by culture analysis. Methodology: Fifty severely curved mesiobuccal canals of mandibular molars were selected and instrumented. Following this, six specimens were selected as control, while 44 canals were contaminated with Enterococcus faecalis strains (ATCC 29212). Specimens were incubated for 21 days at 37 ºC. Then, contaminated specimens were randomly divided into 3 groups (n=14): ProTaper Next (G1), XP-Endo Shaper (G2) and Reciproc Blue (G3). Control Group: Six non-contaminated canals were prepared with one of the 3 file systems (n=2). Microbial samples were obtained before (S1) and after root canal preparation (S2). Two roots were observed using scanning electron microscopy to verify biofilm formation. Quantitative culture analyses of intracanal E. faecalis reduction was performed using CFUs, and the Wilcoxon test was used for intragroup analysis, and intergroup analysis was performed using Kruskal-Wallis test. The level of significance for all analyses was set at P < .05. Results: All systems presented effective bacterial reduction (p<0.05), but still had bacterial growth. ProTaper Next displayed the highest E. faecalis reduction (P<0.05), while XP-Endo Shaper and Reciproc Blue systems presented similar results (P>0.05). ProTaper Next showed the greatest antibacterial action when compared to the XP-Endo Shaper and Reciproc Blue systems. Conclusion: No instrumentation system rendered root canals completely free from bacteria.

Uremia causes dysbiosis-mediated periodontal disease

It is presently unclear why there is a high prevalence of periodontal disease (PD) in individuals living with chronic kidney disease (CKD). By employing three different models in rats and mice, we demonstrate that experimental uremia causes periodontal bone loss. Uremia alters the biochemical composition of saliva and induces progressive dysbiosis of the oral microbiota, with microbial samples from uremic animals displaying reduced overall bacterial growth, increased alpha diversity, reduced abundance of key components of the healthy oral microbiota such as Streptococcus and Rothia, and an increase in minor taxa including those from gram-negative phyla Proteobacteria and Bacteroidetes. We show that transfer of oral microbiota from uremic mice induces PD in germ-free animals, whilst co-housing with healthy animals ameliorates the PD phenotype in rats. Thus, we advocate that periodontal disease should be regarded as a bacterially mediated complication of chronic uremia.

Biodegradation and Microbial Contamination of Limestone Surfaces: An Experimental Study from Batalha Monastery, Portugal

An experimental study was conducted to assess the nature and extent of the biodeterioration of the limestone in the Batalha Monastery in Portugal. Stone fragments covered with microbial biofilms and lichenous crusts were investigated using Optical Microscopy (OM), Low Vacuum Scanning Electron Microscopy with Energy Dispersive Spectroscopy (LV-SEM + EDS), and X-ray micro-Diffractometry (μ-XRD). Microbial samples were collected from the stone surface, cultured, and analyzed with NGS metagenomic DNA test to classify the bacterial communities associated with the formation of the biofilms. Particulate air pollutants collected on Pall GN-6 paper filters using a cascade impactor were characterized by SEM-EDS + NGS. The results showed that lichens play a major role in biodeterioration by promoting both physical and chemical attack on the limestone substrate via hyphae mechanical penetration along calcite inter-crystalline spaces, the dissolution/leaching of calcite minerals, and the precipitation of secondary minerals such as Ca-oxalates within the stone porosity framework. DNA analyses identified the bacterial communities within the biofilms and their relative abundances. Air quality monitoring results suggest that the microbial population colonizing the monastery limestone could at least partially be derived from the dry and wet deposition of airborne biological particles on the stone surfaces and that S, N, and P-rich air pollutants may have provided nutrients and energy for the bacteria communities, thus indirectly facilitating biofilm formation, the growth of a lichenous crusts, and limestone biodeterioration effects.