Rrna Sequencing
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2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Anirudha R. Dixit ◽  
Christina L. M. Khodadad ◽  
Mary E. Hummerick ◽  
Cory J. Spern ◽  
LaShelle E. Spencer ◽  
...  

Abstract Background Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants’ health or productivity. To determine the impact of seed sanitization on the plants’ microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. ‘Outredgeous’) and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli. Result E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment. Conclusion Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.


2021 ◽  
Vol 11 (21) ◽  
pp. 9867
Author(s):  
Mihaela Dumitru ◽  
Dan Cristian Vodnar ◽  
Simon Elemer ◽  
Georgeta Ciurescu ◽  
Mihaela Habeanu ◽  
...  

A total of 15 strains of lactic acid bacteria (LAB) were isolated from the broiler chicken’s gastrointestinal tract. All isolates were phenotypical and genetically identified. Among these isolates, only six were biochemical (API 50 CHL and ABIS soft) and genetically (16S rRNA sequencing) confirmed as Lactobacillus acidophilus, Limosilactobacillus fermentum, Levilactobacillus brevis, and Ligilactobacillus salivarius. Probiotic properties, including tolerance to pH (pH 2.0 and 3.0), bile salts (0.3% oxgall), hemolysis activity, and antibiotic susceptibility, were evaluated. Three isolates of the latter isolates showed high resistance at low pH values (73.74% to 98.20%) and bile salt concentrations (77.89% to 99.49%). The antibiotic test presented 100% resistance of LAB to gentamicin, lincomycin, enrofloxacin, and streptomycin lower than the 0.5 mm inhibition zone diameter. Selected strains (L. acidophilus IBNA 64, L. salivarius IBNA 33, and L. salivarius IBNA 41) were exposed to the spray-drying process based on observable probiotic potential. A maltodextrin-glucose solution was used as a thermoprotectant. After spray drying, a reduction in strain viability was noted (108 to 104 CFU/g). In conclusion, only L. salivarius (IBNA 33 and IBNA 41) could be used as a possible probiotic, and further studies are needed to ensure their safe application in the animal nutrition field with beneficial effects for improving performance and pathogen microorganism control from intestines equilibrating the microbiota composition.


2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Mu-keng Hong ◽  
Hai-hua Liu ◽  
Gui-hong Chen ◽  
Jun-qing Zhu ◽  
Song-yuan Zheng ◽  
...  

Acetaminophen (APAP) hepatotoxicity is the leading cause of acute liver failure in the western world. Oridonin (OD), which is the major active ingredient of the traditional Chinese medicine Rabdosia rubescens, reportedly exerts anti-inflammatory and antioxidative effects. Here, we first find that OD protects against APAP-induced hepatotoxicity. The results of hepatic tissue-associated RNA-seq and metabolomics showed that the protective effects of OD were dependent upon urea cycle regulation. And such regulation of OD is gut microbiota partly dependent, as demonstrated by fecal microbiota transplantation (FMT). Furthermore, using 16S rRNA sequencing, we determined that OD significantly enriched intestinal Bacteroides vulgatus, which activated the nuclear factor erythroid 2-related factor 2 (Nrf2) pathway to regulate redox homeostasis against APAP by urea cycle. In conclusion, our study suggests that the Bacteroides vulgatus-urea cycle-Nrf2 axis may be a potential target for reducing APAP-induced liver injury, which is altered by OD.


Nutrients ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 3656
Author(s):  
Fokhrul Hossain ◽  
Samarpan Majumder ◽  
Justin David ◽  
Bruce A. Bunnell ◽  
Lucio Miele

Triple-negative breast cancer (TNBC) is an aggressive, molecularly heterogeneous subtype of breast cancer. Obesity is associated with increased incidence and worse prognosis in TNBC through various potential mechanisms. Recent evidence suggests that the gut microbiome plays a central role in the progression of cancer, and that imbalances or dysbiosis in the population of commensal microbiota can lead to inflammation and contribute to tumor progression. Obesity is characterized by low-grade inflammation, and gut dysbiosis is associated with obesity, chronic inflammation, and failure of cancer immunotherapy. However, the debate on what constitutes a “healthy” gut microbiome is ongoing, and the connection among the gut microbiome, obesity, and TNBC has not yet been addressed. This study aims to characterize the role of obesity in modulating the gut microbiome in a syngeneic mouse model of TNBC. 16S rRNA sequencing and metagenomic analyses were performed to analyze and annotate genus and taxonomic profiles. Our results suggest that obesity decreases alpha diversity in the gut microbiome. Metagenomic analysis revealed that obesity was the only significant factor explaining the similarity of the bacterial communities according to their taxonomic profiles. In contrast to the analysis of taxonomic profiles, the analysis of variation of functional profiles suggested that obesity status, tumor presence, and the obesity–tumor interaction were significant in explaining the variation of profiles, with obesity having the strongest correlation. The presence of tumor modified the profiles to a greater extent in obese than in lean animals. Further research is warranted to understand the impact of the gut microbiome on TNBC progression and immunotherapy.


2021 ◽  
Author(s):  
Hye Jin Jang ◽  
Ji Yeon Choi ◽  
Kangjoon Kim ◽  
Seung Hyun Yong ◽  
Yeon Wook Kim ◽  
...  

Abstract Background: Lung cancer is the primary cause of cancer-related deaths worldwide. The human lung serves as a niche to a unique and dynamic bacterial community that is related to the development of multiple diseases. Here, we investigated the differences in the lung microbiomes of patients with lung cancer. Methods: 16S rRNA sequencing was performed to evaluate the respiratory tract microbiome present in the bronchoalveolar lavage fluid. Patients were stratified based on programmed death-ligand 1 (PD-L1) expression levels and immunotherapy responses. Results: In total, 84 patients were prospectively analyzed, of which 59 showed low (<10%), and 25 showed high (>10%) PD-L1 expression levels. The alpha and beta diversities did not significantly differ between the two groups. Veillonella dispar was dominant in the high-PD-L1 group; the population of Neisseria was significantly higher in the low-PD-L1 group than in the high-PD-L1 group. In the immunotherapy responder group, V. dispar was dominant, while Haemophilus influenzae and Neisseria perflava were dominant in the non-responder group. Conclusion: The abundances of Neisseria and V. dispar differed significantly in relation to PD-L1 expression levels and immunotherapy responses. Thus, these two genera may be considered targets for lung cancer immunotherapy.


2021 ◽  
Vol 12 ◽  
Author(s):  
Honglin Yan ◽  
Wenzhuo Wei ◽  
Luga Hu ◽  
Yong Zhang ◽  
Hongfu Zhang ◽  
...  

A biphasic feeding regimen exerts an improvement effect on feed efficiency of pigs. While gut microbiome and metabolome are known to affect the host phenotype, so far the effects of reduced feeding frequency on fecal microbiota and their metabolism in pigs remain unclear. Here, the combination of 16S rRNA sequencing technique as well as untargeted and targeted metabolome analyses was adopted to investigate the fecal microbiome and metabolome of growing–finishing pigs in response to a biphasic feeding [two meals per day (M2)] pattern. Sixty crossbred barrows were randomly assigned into two groups with 10 replicates (three pigs/pen), namely, the free-access feeding group (FA) and the M2 group. Pigs in the FA group were fed free access while those in the M2 group were fed ad libitum twice daily for 1 h at 8:00 and 18:00. Results showed that pigs fed biphasically exhibited increased feed efficiency compared to FA pigs. The Shannon and Simpson indexes were significantly increased by reducing the feeding frequency. In the biphasic-fed pigs, the relative abundances of Subdoligranulum, Roseburia, Mitsuokella, and Terrisporobacter were significantly increased while the relative abundances of unidentified_Spirochaetaceae, Methanobrevibacter, unidentified_Bacteroidales, Alloprevotella, Parabacteroides, and Bacteroides were significantly decreased compared to FA pigs. Partial least-square discriminant analysis (PLS-DA) analysis revealed an obvious variation between the FA and M2 groups; the differential features were mainly involved in arginine, proline, glycine, serine, threonine, and tryptophan metabolism as well as primary bile acid (BA) biosynthesis. In addition, the changes in the microbial genera were correlated with the differential fecal metabolites. A biphasic feeding regimen significantly increased the abundances of primary BAs and secondary BAs in feces of pigs, and the differentially enriched BAs were positively correlated with some specific genera. Taken together, these results suggest that the improvement effect of a reduced feeding frequency on feed efficiency of pigs might be associated with the altered fecal microbial composition and fecal metabolite profile in particular the enlarged stool BA pool.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yanli Xiong ◽  
Xiaopeng Yang ◽  
Yi Xiong ◽  
Chaohui Xiong ◽  
Wenlong Gou ◽  
...  

AbstractThe popularized application of annual ryegrass—maize rotation (ARMR) in southern China has been proposed to fully utilize the farmlands and to increase forage yield and quality. Herein, one growth cycle of ARMR was conducted and soil bacteria were analyzed by 16S rRNA sequencing for control (CK), after the preceding crop (monoculture, or mixed sowing of annual ryegrass and oat) and the successive crop (maize). Our results indicated that the α-diversity of soil bacteria was changed in the ARMR system, which was related to the activity of urease and available phosphatase. The mixed sowing of annual ryegrass and oat in preceding crop could improve the yield and quality, while it was accompanied by unbalanced soil community. With the increased sowing proportion of oat to annual ryegrass, the soil pH increased while the soil available phosphatase decreased. The ARMR system was found to benefit the soil microenvironment by increasing the beneficial soil bacteria and enzyme activity or decreasing the harmful soil bacteria. Considering the soil bacteria α-diversity index and physicochemical properties comprehensively, the recommended sowing regime is the mixed sowing of M2 (22.5 kg·hm−2 annual ryegrass with 75 kg·hm−2 oat).


Author(s):  
Changchang Ye ◽  
Meng You ◽  
Ping Huang ◽  
Zhongyi Xia ◽  
Allan Radaic ◽  
...  

Abstract Objectives The objective of this study was to examine the association between the oral microbiome and pregnancy outcomes, specifically healthy or preterm low birth weight (PLBW) in individuals with and without periodontal disease (PD). Material and methods In this prospective clinical trial, we recruited 186 pregnant women, 17 of whom exhibited PD and delivered PLBW infants (PD-PLBW group). Of the remaining women, 155 presented PD and delivered healthy infants; 18 of these subjects with similar periodontal condition and age matched to the PD-PLBW group, and they became the PD-HD group. From the total group, 11 women exhibited healthy gingiva and had a healthy delivery (HD) and healthy infants (H-HD group), and 3 exhibited healthy gingiva and delivered PLBW infants (H-PLBW group). Periodontal parameters were recorded, and subgingival plaque and serum were collected during 26–28 gestational weeks. For the plaque samples, microbial abundance and diversity were accessed by 16S rRNA sequencing. Results Women with PD showed an enrichment in the genus Porphyromonas, Treponema, and Filifactor, whereas women with healthy gingiva showed an enrichment in Streptococcus, Actinomyces, and Corynebacterium, independently of the birth status. Although no significant difference was found in the beta diversity between the 4 groups, women that had PLBW infants presented a significantly lower abundance of the genus Neisseria, independently of PD status. Conclusion Lower levels of Neisseria align with preterm low birth weight in pregnant women, whereas a higher abundance of Treponema, Porphyromonas, Fretibacterium, and Filifactor and a lower abundance of Streptococcus may contribute to periodontal disease during pregnancy. Clinical relevance The oral commensal Neisseria have potential in the prediction of PLBW.


2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 444-444
Author(s):  
YangYi Hao ◽  
Shuai Huang ◽  
Shengli Li

Abstract The objective was to understand the effects of diet and age on the rumen bacterial community and function, 48 dairy cattle were selected. Rumen fluid samples were collected from each animal at 1.5 (1.5M, milk and starter diet, n=8), 6 (6M, starter and oat grass, n=8), 9 (9M, high fiber diet, n=8), 18 (18M, high fiber diet, n=8), 23 (23M, high fiber diet, n=8) and 27 (27M, high grain diet, n=8) months old. The acetate/propionate ratio (A/P) at M9, M18, and M23 were significantly higher than M27 and M1.5 (P &lt; 0.05), while the A/P at M6 was lower than others (P &lt; 0.05). The total volatile fatty acid at M23 and M27 was higher than others (P &lt; 0.05). The urease at M18 was significantly lower than M1.5, M6, and M9 (P &lt; 0.05), and the xylanase at M18 was significantly higher than M1.5, M23, and M27 (P &lt; 0.05). 16S rRNA sequencing data and the Linear discriminant analysis showed that thirty-three bacteria were identified as biomarkers among ages and diets. The age and diet contributed 7.98% and 32.49% to the rumen bacteria community using the variation partitioning approach analysis. The norank_f_p-251-o5 was significantly and positively correlated with age (r = 0.83, P &lt; 0.01), while Eubacterium was significantly and negatively correlated with age (r = -0.84, P &lt; 0.01). Dietary fiber showed a strong correlation (r &gt; 0.80, P &lt; 0.01) with Lachnospiraceae, NK4A214_group, Saccharofermentans, Clostridia, Pseudobutyrivibrio Bacteroidales_UCG-001. These genera also negatively correlated with dietary crude protein and starch (r &lt; - 0.80, P &lt; 0.01). All these bacteria were significantly correlated with A/P, acetate, and urease (r &gt; 0.5, P &lt; 0.05). These findings collectively indicated that diet drives the great ability to shape the rumen bacteria community and function than age.


2021 ◽  
Author(s):  
Batosz Czech ◽  
Joanna Szyda ◽  
Kai Wang ◽  
Hanpeng Luo ◽  
Yachun Wang

Humans have been influencing climate changes by burning fossil fuels, farming livestock, and cutting down rainforests, which has led to global temperature rise. This problem of global warming affects animals by causing heat stress, which negatively affects their health, biological functions, and reproduction. On the molecular level, it has been proved that heat stress changes the expression level of genes and therefore causes changes in proteome and metabolome. The importance of a microbiome in many studies showed that it is considered as individuals' 'second genome'. Physiological changes caused by heat stress may impact the microbiome composition. In this study, we identified fecal microbiota associated with heat stress that was quantified by three metrics - rectal temperature, drooling, and respiratory scores and represented by their Estimated Breeding Values. For this purpose, the 16S rRNA sequencing technique was used. We analyzed the microbiota from 136 fecal samples of Chinese Holstein cows through a 16S rRNA gene sequencing approach. Sequence data were processed using a pipeline involving QIIME2 software together with SILVA database. Statistical modeling was performed using a negative binomial regression. The analysis revealed the total number of 24 genera and 12 phyla associated with heat stress metrics. Rhizobium and Pseudobutyrivibrio turned out to be the most significant genera, while Acidobacteria and Gemmatimonadetes were the most significant phyla. Phylogenetic analysis revealed that that three heat stress indicators quantify different metabolic ways of animals' reaction to heat stress. Other studies already identified that those genera had significantly increased abundance in mice exposed to stressor-induced changes. Moreover, identified microbiota significantly associated with heat stress measures were mostly mesophilic, so their association seems to be due to heat stress-induced secondary, metabolic changes, and not directly by temperature. Moreover, high fold changes of many genera suggest that they may be used as biomarkers for monitoring the level of heat stress in cattle.


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