Summary
Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (containing 11 or 27 marine 16S clones), showing alternative primers 515F-Y (5′-GTGYCAGCMGCCGCGGTAA) and 926R (5′-CCGYCAATTYMTTTRAGTTT) yield more accurate estimates of mock community abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, and amplify eukaryotic 18S rRNA. Mock communities amplified with 515F-Y/926R yielded closer observed community composition versus expected (r2 = 0.95) compared with 515F-Y/806R (r2 ∼ 0.5). Unexpectedly, biases with 515F-Y/806R against SAR11 in field samples (∼4–10-fold) were stronger than in mock communities (∼2-fold). Correcting a mismatch to Thaumarchaea in the 515F-C increased their apparent abundance in field samples, but not as much as using 926R rather than 806R. With plankton samples rich in eukaryotic DNA (> 1 μm size fraction), 18S sequences averaged ∼17% of all sequences. A single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification. We show that beyond in silico predictions, testing with mock communities and field samples is important in primer selection.

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

结节病易误诊,据王洪武等~([1])收集国内18篇关于此病误诊的文献,误诊率高达63.2%,当然有误诊就会有误治,如孙永昌等~([2])报道26例结节病在影像学检查诊断的第一印象中拟诊结核5例,其中就有2例完成规范的抗结核治疗,为此应引起临床对本病诊治的重视。

Sarcoidosis

Relation between the gut microbiota and human health is being increasingly recognised It is now well established that a healthy gut flora is largely responsible for overall health of the host The normal human gut microbiota comprises of two major phyla, namely Bacteroidetes and Firmicutes Though the gut microbiota in an infant appears haphazard, it starts resembling the adult flora by the age of 3 years Nevertheless, there exist temporal and spatial variations in the microbial distribution from esophagus to the rectum all along the individual's life span Developments in genome sequencing technologies and bioinformatics have now enabled scientists to study these microorganisms and their function and microbe-host interactions in an elaborate manner both in health and disease The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation, and protection against pathogens Several factors play a role in shaping the normal gut microbiota They include (1) the mode of delivery (vaginal or caesarean); (2) diet during infancy (breast milk or formula feeds) and adulthood (vegan based or meat based); and (3) use of antibiotics or antibiotic like molecules that are derived from the environment or the gut commensal community A major concern of antibiotic use is the long-term alteration of the normal healthy gut microbiota and horizontal transfer of resistance genes that could result in reservoir of organisms with a multidrug resistant gene pool

Role of the normal gut microbiota

Nutrient requirements of beef cattle

Mineral trioxide aggregate: a comprehensive literature review--Part I: chemical, physical, and antibacterial properties.

Status of the phylogenetic diversity census of ruminal microbiomes

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

Methanogenic archaea reside primarily in the rumen and the lower segments of the intestines of ruminants, where they utilize the reducing equivalents derived from rumen fermentation to reduce carbon dioxide, formic acid, or methylamines to methane (CH4). Research on methanogens in the rumen has attracted great interest in the last decade because CH4 emission from ruminants contributes to global greenhouse gas emission and represents a loss of feed energy. Some DNA-based phylogenetic studies have depicted a diverse and dynamic community of methanogens in the rumen. In the past decade, researchers have focused on elucidating the underpinning that determines and affects the diversity, composition, structure, and dynamics of methanogen community of the rumen. Concurrently, many researchers have attempted to develop and evaluate interventions to mitigate enteric CH4 emission. Although much work has been done using plant secondary metabolites, other approaches such as using nitrate and 3-nitrooxy propanol have also yielded promising results. Most of these antimethanogenic compounds or substances often show inconsistent results among studies and also lead to adverse effects on feed intake and digestion and other aspects of rumen fermentation when fed at doses high enough to achieve effective mitigation. This review provides a brief overview of the rumen methanogens and then an appraisal of most of the antimethanogenic compounds and substances that have been evaluated both in vitro and in vivo. Knowledge gaps and future research needs are also discussed with a focus on methanogens and methane mitigation.

/pdf/rumen-methanogens-and-mitigation-of-methane-emission-by-anti-4r6c11m3qp.pdf

Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances

Peritumoral edema (PTE) in meningioma occurs variably and can adversely affect the clinical course. Moreover, the etiology of PTE in meningioma is not well documented. To examine possible correlations with PTE, the authors investigated the clinical parameters and the expressions of vascular endothelial growth factor (VEGF), matrix metalloproteinases (MMPs), and their inhibitors (TIMPs) in 20 meningiomas. The estimation of tumor volume (V(T)) and edema volume (V(E)) was done using Osiris software with magnetic resonance images and the edema index (EI) was calculated. The expression of VEGF, MMP, and TIMP were estimated in all 20 meningiomas by immunohistochemical staining, Western blotting, zymography, and laser densitometry. Tumor location was closely related with PTE. Meningiomas of the frontal lobe or the frontotemporal base had large PTEs, whereas those of the occipitoparietal lobe, posterior fossa or petroclivus were small. The level of VEGF expression bore correlation with the extent of PTE but not with histologic malignancy. MMP-2 and -9 were detected in 100% of meningiomas by zymography. The levels of MMP-9 were significantly elevated in moderate to severe edema (EI > 1.0) group (p < 0.05) whereas those of MMP-2 were elevated in minimal to mild edema (EI < 1.0) group. TIMP-1 and -2 were detected in 19 (95%) and 12 (60%) of meningiomas respectively and their presence had no significant correlations statistically with PTE between two groups (p = 0.190 and 0.089, respectively). Meningiomas with severe PTE expressed high levels of VEGF and MMP-9 and low levels of MMP-2. The expressions of MMP-2, -9, and TIMPs as well as VEGF in meningioma suggests that they are strongly related with the presence of PTE in meiningiomas, and that they might play the important role in the formation of PTE in meningiomas.

Correlation of clinical and biological parameters with peritumoral edema in meningioma.

Objective This study compared the chemical constitution, radiopacity, and biocompatibility of Portland cement containing bismuth oxide (experimental cement) with those of Portland cement and mineral trioxide aggregate (MTA). Study design The chemical constitution of materials was determined by scanning electron miscroscopy and energy-dispersive X-ray analysis. The radiopacity of the materials was determined using the ISO/6876 method. The biocompatibility of the materials was tested by MTT assay and tissue reaction. Results The constitution of all materials was similar. However, the Portland cement and experimental cement were more irregular and had a larger particle size than MTA. The radiopacity of the experimental cement was similar to MTA. The MTT assay revealed MTA to have slightly higher cell viability than the other materials. However, there were no statistically significant differences between the materials, with the exception of MTA at 24 h. There was no significant difference in the tissue reaction between the experimental groups. Conclusions These results suggest that the experimental cement may be used as a substitute for MTA.

https://www.endoexperience.com/documents/PortlandcementandbismuthoxideOOOOE2009.pdf

Min-Seok Kim

Papers

Status of the phylogenetic diversity census of ruminal microbiomes

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

Rumen methanogens and mitigation of methane emission by anti-methanogenic compounds and substances

Correlation of clinical and biological parameters with peritumoral edema in meningioma.

Chemical composition, radiopacity, and biocompatibility of Portland cement with bismuth oxide.