scholarly journals Conjunctival Sac Microbiome in Infectious Conjunctivitis

2021 ◽  
Vol 9 (10) ◽  
pp. 2095
Author(s):  
Yasser Mohamed ◽  
Masafumi Uematsu ◽  
Yoshitomo Morinaga ◽  
Hien-Anh Thi Nguyen ◽  
Michiko Toizumi ◽  
...  

Acute bacterial conjunctival infections are common, and this study identified the conjunctival bacterial community in infectious conjunctivitis cases seen at the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. The study included 47 randomly selected patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constituted 92% of all sequences (Firmicutes (35%), Actinobacteria (31%), and Proteobacteria (26%)). At the genus level, there were 12 common genera that constituted about 61% of all sequence reads. Seven of those genera were common (Streptococcus (10%), Cutibacterium (10%), Staphylococcus (7%), Nocardioides (7%), Corynebacterium 1 (5%), Anoxybacillus (5%), and Acinetobacter (5%)), which encompassed 49% of all reads. As for diversity analysis, there was no difference on PERMANOVA analysis (unweighted UniFrac) for sex (p = 0.087), chemosis (p = 0.064), and unclassified eyedrops (p = 0.431). There was a significant difference in cases with bilateral conjunctivitis (p = 0.017) and for using antibiotics (p = 0.020). Of the predominant phyla, Firmicutes had the highest abundance in bacterial conjunctivitis in this study. Pseudomonas as a resident commensal microbiota may have an important role in the prevention of infection.

2020 ◽  
Author(s):  
Yasser Helmy Mohamed ◽  
Masafumi Uematsu ◽  
Yoshitomo Morinaga ◽  
Hien-Anh Nguyen ◽  
Michiko Toizumi ◽  
...  

Abstract Background To determine the conjunctival bacterial community among the infectious conjunctivitis cases attending the outpatient clinic of Khanh Hoa General Hospital in Nha Trang, Vietnam from October 2016 through December 2017. Of all, 50 randomly selected samples using a computer generated random number list were included for microbiome identification. Conjunctival swabs were collected and tested using conventional culture, PCR, and 16S ribosomal RNA sequencing. Results The study included randomly selected 47 patients. More than 98% of all DNA reads represented five bacterial phyla. Three of these phyla constitute 92% of all sequences [Firmicutes (35%), Actinobacteria (31%), and Proteobacteria (26%)]. At the genus level, there were twelve common genera constituted about 61% of all the sequence reads. Seven of those genera were common [Streptococcus (10%), Cutibacterium (10%), Staphylococcus (7%), Nocardioides (7%), Corynebacterium 1 (5%), Anoxybacillus (5%), and Acinetobacter (5%)], which encompassed 49% of all reads. As for diversity analysis, there was no difference in PERMANOVA analysis (Unweighted UniFrac) for sex (P = 0.087), chemosis (P = 0.064) and unclassified eyedrops (P = 0.431). There was no difference in PERMANOVA analysis for pain (P = 0.315) and itching (P = 0.133). There was a statistical significant difference in cases with bilateral conjunctivitis (P = 0.017) and for using antibiotics (P = 0.020). Conclusion Firmicutes among the predominant phyla has the highest abundance in bacterial conjunctivitis in our study. Pseudomonas as a resident commensal microbiota has an important role for prevention of infection.


Agriculture ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1224
Author(s):  
Mohammad Murtaza Alami ◽  
Qiuling Pang ◽  
Zedan Gong ◽  
Tewu Yang ◽  
Daiqun Tu ◽  
...  

Chinese goldthread (Coptis chinensis Franch.) represents one of the most important medicinal plants with diverse medicinal applications, but it easily suffers from continuous cropping obstacles in the plantation. In this study, we have selected eight different continuously cropped fields with C. chinensis and fallow field, providing detailed information regarding the diversity and composition of the rhizospheric bacterial communities. We have found a significant difference between fallow field (LH) and other continuously cropped fields in soil pH; the total content of nitrogen, phosphorus, and potassium; and soil enzyme activities. The results indicate that continuous cropping had a significant effect on soil physicochemical properties and enzyme activities under different plant cultivations. The relative abundance of bacterial phyla was significantly altered among the fields; for example, proteobacteria and Actinobacteria were observed to be higher in continuous cropping of maize (HY6) and lower in sweet potato continuous cropping (HH). Alpha diversity analysis showed that different plants with different years of continuous cropping could change the diversity of bacterial communities, among which the effect of maize and Polygonum multiflorum continuous cropping were most significant. Principle coordinate analysis (PCoA) showed that continuously cropped C. chinensis (LZ) and cabbage continuously cropped for 2 years (HS) were slightly clustered together and separated from LH and others. The results showed that the similarity of the bacterial community in the same crop rotation was higher, which further indicated that the bacterial community structure was significantly altered by the continuous cropping system and plant species. Our study provides a foundation for future agricultural research to improve microbial activity and increase crops/cash-crops productivity under a continuous cropping system and mitigate continuous cropping obstacles.


2021 ◽  
Vol 108 (Supplement_2) ◽  
Author(s):  
A Fung ◽  
A Ward ◽  
K Patel ◽  
M Krkovic

Abstract Introduction Infection is a major complication of open fractures. Antibiotic-impregnated calcium sulfate (AICS) beads are widely used as an adjuvant to systemic antibiotics. Whilst their efficacy in the secondary prevention of infection is established, we present the first retrospective study evaluating AICS beads in the primary prevention of infection in open fractures. Method 214 open femur and tibia fractures in 207 patients were reviewed over a seven-year period. 148 fractures received only systemic antibiotic prophylaxis. 66 fractures also received AICS beads. The occurrence of acute infection (wound infection and acute osteomyelitis) was recorded, as well as that of long-term complications (chronic osteomyelitis, non-union and death). Results Fractures that received AICS with systemic antibiotics had an overall acute infection rate of 42% (28/66), compared to 43% (63/148) in fractures that received only systemic antibiotics (p > 0.05). There was no significant difference in infection rate even when fractures were stratified by Gustilo-Anderson grade. There was also no significant difference in the rate of long-term complications. Conclusions Our results indicate that the adjuvant use of AICS beads is not effective for the primary prevention of acute infection or long-term complications in open leg fractures. Further research is needed to elucidate the factors influencing the outcomes of AICS use.


2021 ◽  
Vol 17 ◽  
pp. 117693432199635
Author(s):  
Daoxin Liu ◽  
Pengfei Song ◽  
Jingyan Yan ◽  
Haijing Wang ◽  
Zhenyuan Cai ◽  
...  

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.


2014 ◽  
Vol 99 (1) ◽  
pp. 469-476 ◽  
Author(s):  
Huagui Liu ◽  
Houlong He ◽  
Changhe Cheng ◽  
Jinli Liu ◽  
Ming Shu ◽  
...  

Forests ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 121
Author(s):  
Tize Xia ◽  
Lushuang Li ◽  
Bin Li ◽  
Peitong Dou ◽  
Hanqi Yang

The previous studies show soil microbes play a key role in the material and nutrient cycles in the forest ecosystem, but little is known about how soil microbes respond to plant distribution, especially in the soil bacterial community in woody bamboo forests. Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang, 2007 is known as the only bamboo species producing shoots all year round in natural conditions. Endemic to the Dawei mountain in Yunnan of China, this species is a good case to study how soil bacteria respond to plant endemic distribution. In this work, we assayed the soil chemical properties, enzyme activity, changes in the bacterial community along the distribution range of the C. pingbianense forest. The results showed that soil nutrients at the range edge were nitrogen-rich but phosphorus-deficient, and soil pH value and soil urease activity were significantly lower than that of the central range. No significant difference was detected in soil bacterial diversity, community composition, and function between the central and marginal range of C. pingbianense forest. Notably, the relative abundance of heterotrophy bacteria, such as Variibacter and Acidothermus, in the soil of the C. pingbianense forest was significantly higher than that of the outside range, which may lead to a higher soil organic carbon mineralization rate. These results imply that abundant heterotrophy bacteria were linked to the endemism and full-year shooting in C. pingbianense. Our study is amongst the first cases demonstrating the important role of heterotrophy bacteria in the distribution formation of endemic woody bamboos in special soil habitats, and provides insight into germplasm conservation and forest management in woody bamboos.


2021 ◽  
Vol 12 ◽  
Author(s):  
Lifeng Zhu ◽  
Wei Zhu ◽  
Tian Zhao ◽  
Hua Chen ◽  
Chunlin Zhao ◽  
...  

An increasing number of studies have shown that warming also influences the animal gut microbiome (altering the community structure and decreasing its diversity), which might further impact host fitness. Here, based on an analysis of the stomach and gut (the entire intestine: from the anterior intestine to the cloaca) microbiome in laboratory larva of giant salamanders (Andrias davidianus) under different living water temperatures (5, 15, and 25°C) at two sample time points (80 and 330 days after the acclimation), we investigated the potential effect of temperature on the gastrointestinal microbiome community. We found the significant Interaction between sampling time and temperature, or type (stomach and gut) on Shannon index in the gastrointestinal microbiome of the giant salamanders. We also found the significant difference in Shannon index among temperature groups within the same sample type (stomach or gut) at each sample time. 10% of variation in microbiome community could be explained by temperature alone in the total samples. Both the stomach and gut microbiomes displayed the highest similarity in the microbiome community (significantly lowest pairwise unweighted Unifrac distance) in the 25-degree group between the two sampling times compared to those in the 5-degree and 15-degree groups. Moreover, the salamanders in the 25°C treatment showed the highest food intake and body mess compared to that of other temperature treatments. A significant increase in the abundance of Firmicutes in the gastrointestinal microbiome on day 330 with increasing temperatures might be caused by increased host metabolism and food consumption. Therefore, we speculate that the high environmental temperature might indirectly affect both alpha and beta diversity of the gastrointestinal microbiome.


2019 ◽  
Author(s):  
William J. Watterson ◽  
Melikhan Tanyeri ◽  
Andrea R. Watson ◽  
Candace M. Cham ◽  
Yue Shan ◽  
...  

AbstractTraditional cultivation approaches in microbiology are labor-intensive, low-throughput, and often yield biased sampling of taxa due to ecological and evolutionary factors. New strategies are needed to enable ample representation of rare taxa and slow-growers that are outcompeted by fast-growing organisms. We developed a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts droplets based on colony density. We applied our strategy to mouse and human gut microbiomes and used 16S ribosomal RNA gene amplicons to characterize taxonomic composition of cells grown using different media. We found up to 4-fold increase in richness and larger representation of rare taxa among cells grown in droplets compared to conventional culture plates. Automated sorting of droplets for slow-growing colonies further enhanced the relative abundance of rare populations. Our method improves the cultivation and analysis of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.


1989 ◽  
Vol 1 (1) ◽  
pp. 12-15 ◽  
Author(s):  
Lorraine J. Hoffman

The conventional culture method was compared to coagglutination for detection of Actinobacillus (Haemophilus) pleuropneumoniae in 425 sets of pig lungs. Sera from the same animals were evaluated for antibodies to A. pleuropneumoniae by the complement fixation (CF) test. All samples were collected at 2 packing plants in Iowa. In 2 nonvaccinated herds with no history of respiratory disease, the difference between standard culture results and coagglutination was highly significant ( P < 0.001). None of the 57 pigs in this group were positive for A. pleuropneumoniae by conventional culture, but 7 were positive by the coagglutination test. There were 15 animals with CF titers between 1:8 and 1:32. Animals from 6 herds vaccinated for A. pleuropneumoniae and without recent respiratory problems were evaluated. One out of 118 animals tested was positive for A. pleuropneumoniae by standard culture as compared to 9 positive by coagglutination. The difference in positive results between culture and coagglutination was highly significant ( P < 0.001). Twenty-eight animals had CF titers to A. pleuropneumoniae (1:4 to ≥ 1: 128). Two hundred fifty lungs and sera samples were collected from 7 herds which had recently experienced varying degrees of respiratory disease. Thirty-nine lungs were positive for A. pleuropneumoniae by culture and 182 were positive by coagglutination. The number of positives detected by coagglutination was significantly different ( P < 0.001) from the number positive by culture. There were 172 animals with antibody titers ranging from suspect to ≥ 1:128. There were significantly fewer positive animals detected by standard culture than with the CF test ( P < 0.001). There was no significant difference between coagglutination results and CF titers when a titer of 1:4 was used as the positive threshold.


Sign in / Sign up

Export Citation Format

Share Document