scholarly journals The Effect of Spatial Location of Fermentation Pit on Prokaryotic Community Diversity in Pit Mud for Chinese Strong-Flavor Baijiu Production

2021 ◽  
Author(s):  
Xiaolong Hu ◽  
Dahong Feng ◽  
Miao Yu ◽  
Sifan Wang ◽  
Yong Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Location ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
Total Acid ◽  
Α Diversity ◽  
Physicochemical Factors ◽  
Pit Mud ◽  
Significant Difference ◽  
Dominant Bacteria

Abstract Background Chinese strong-flavor baijiu (CSFB) accounts for more than 70% of all Chinese liquor markets. Diverse microbes in pit mud found in the fermentation pit play a key role in CSFB production. However, the effect of spatial location on the diversity and structure of the microbial community in pit mud is still poorly understood Results Prokaryotic microbes in different pit mud（4- and 40-year）were analyzed by using Illumina MiSeq sequencing of 16S rRNA gene. The samples were collected from pit mud that was 4 and 40 years old in the top, middle, and under parts of the cellar walls and at the bottom of them. The results showed there was no significant difference (p>0.05) in the physicochemical factors, the Observed OTU, and α-diversity between the pit mud of two different ages. The index of the 4-year-old pit mud was lower (except for total acid, which was higher than) than that of the 40-year-old pit mud. The pH, total acid, Observed OTU, Chao 1, ACE in the 4-year-old pit mud (in the top and middle part of the cellar wall) and the 40-year-old pit mud(in the top part of the cellar wall) had significant (p<0.05) difference. At the phylum level, Firmicutes (56.70%) and Bacteroidetes (26.56%) accounted for more than 80% of the overall level. For the 4-year-old pit mud sample, the dominant genuses at each location were Proteiniphilum, Lactobacillus, and Caproiciproducens, while for the 40-year-old pit mud, there were 10 common genuses accounted for more than 50% of the dominant genuses in different pit mud belong to Clostridia. The RDA analysis results showed that 85.71% of the dominant bacteria positively correlated with pH, and especially the most correlated with the total acid and available phosphorus, so its content was significantly related to the dominant bacteria (p<0.01). Therefore, it inferred that the total acid and available phosphorus were the main physicochemical factors that affected the spatial distribution of prokaryotic microbial communities in the pit mud of cellars from the liquor distillery. Conclusions Comparing the young pit mud and the old pit mud, the structure and physicochemical factors of the prokaryotic microbial community in pit mud from Henan liquor-making company changed, and the changes occurred in the spatial location of different pits. Clostridia, which accounted for more than 50% of all types of pit mud, were responsible for the effect of total acid and available phosphorus on the microbial community. Based on the above, it provides a theoretical basis for Henan liquor-making companies in maintaining pit mud. Keywords: fermentation pit mud; spatial heterogeneity; microbial community; physicochemical factors; Chinese strong-flavor Baijiu.

scholarly journals Illuminating Anaerobic Microbial Community and Cooccurrence Patterns across a Quality Gradient in Chinese Liquor Fermentation Pit Muds

2016 ◽  
Vol 82 (8) ◽  
pp. 2506-2515 ◽  
Author(s):  
Xiaolong Hu ◽  
Hai Du ◽  
Cong Ren ◽  
Yan Xu
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Variable Region ◽  
Illumina Miseq ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
High Quality ◽  
Content Type ◽  
Anaerobic Microorganisms ◽  
Pit Mud

ABSTRACTFermentation pit mud, an important reservoir of diverse anaerobic microorganisms, is essential for Chinese strong-aroma liquor production. Pit mud quality, according to its sensory characteristics, can be divided into three grades: degraded, normal, and high quality. However, the relationship between pit mud microbial community and pit mud quality is poorly understood, as are microbial associations within the pit mud ecosystem. Here, microbial communities at these grades were compared using Illumina MiSeq sequencing of the variable region V4 of the 16S rRNA gene. Our results revealed that the pit mud microbial community was correlated with its quality and environmental factors. Species richness, biodiversity, and relative and/or absolute abundances ofClostridia,Clostridium kluyveri,Bacteroidia, andMethanobacteriasignificantly increased, with corresponding increases in levels of pH, NH4+, and available phosphorus, from degraded to high-quality pit muds, while levels ofLactobacillus, dissolved organic carbon, and lactate significantly decreased, with normal samples in between. Furthermore, 271 pairs of significant and robust correlations (cooccurrence and negative) were identified from 76 genera using network analysis. Thirteen hubs of cooccurrence patterns, mainly under theClostridia,Bacteroidia,Methanobacteria, andMethanomicrobia, may play important roles in pit mud ecosystem stability, which may be destroyed with rapidly increased levels of lactic acid bacteria (Lactobacillus,Pediococcus, andStreptococcus). This study may help clarify the relationships among microbial community, environmental conditions, and pit mud quality, allow the improvement of pit mud quality by using bioaugmentation and controlling environmental factors, and shed more light on the ecological rules guiding community assembly in pit mud.

Organotrophic and Mixotrofic Sulfur Oxidation in an Acidic Salt Flat in Northern Chile

2015 ◽  
Vol 1130 ◽  
pp. 63-66 ◽  
Author(s):  
Lorena Escudero ◽  
Jonathan Bijman ◽  
Guajardo M. Mariela ◽  
Juan José Pueyo Mur ◽  
Guillermo Chong ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Composition ◽  
Iron Concentration ◽  
Rrna Gene ◽  
Salt Flat ◽  
Significant Difference ◽  
Acidic Salt ◽  
The 16S Rrna Gene

To understand the microbial community inhabiting in an acidic salt flat the phylogenetic diversity and the geochemistry of this system was compared to acid mine drainage (AMD) systems. The microbial community structure was assessed by DNA extraction/PCR/DGGE and secuencing for the 16S rRNA gene and the geochemistry was analyzed using several approaches. Prediction of metagenome functional content was performed from the 16S rRNA gene survey using the bioinformatics software package Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). The geochemical results revealed a much lower iron concentration in the salt flat than in AMD systems (39 and 21804 mg L-1, respectively) and a significant difference in chloride levels. Sequences inferred to be from potential sulfur metabolizing organisms constituted up to 70% of the microbial community in the acidic salt flat meanwhile predominat iron-metabolizing acidophile populations were reported in AMD systems. Interestingly, the microbial assemblage in the acidic salt flat was dominated by mixotrophic and organotrophic sulfur oxidizers as well as by photoautotrophic acidophiles. Our results suggests that the salt concentration in Salar de Gorbea (average Cl-= 40 gL-1) is in the limit for the occurrence of chemolithotrophic oxidation of sulfur compounds. In addition, the investigation allows concluding that salinity rather than extremes of pH is the major environmental determinant of microbial community composition.

Sputum neutrophil elastase associates with microbiota and Pseudomonas aeruginosa in bronchiectasis

2020 ◽  
Vol 56 (4) ◽  
pp. 2000769 ◽  
Author(s):  
Martina Oriano ◽  
Andrea Gramegna ◽  
Leonardo Terranova ◽  
Giovanni Sotgiu ◽  
Imran Sulaiman ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Real Time ◽  
Shannon Entropy ◽  
Real Time Pcr ◽  
Neutrophil Elastase ◽  
Stable State ◽  
Rrna Gene ◽  
Respiratory Pathogens ◽  
Α Diversity ◽  
Significant Difference

IntroductionNeutrophilic inflammation is a major driver of bronchiectasis pathophysiology, and neutrophil elastase activity is the most promising biomarker evaluated in sputum to date. How active neutrophil elastase correlates with the lung microbiome in bronchiectasis is still unexplored. We aimed to understand whether active neutrophil elastase is associated with low microbial diversity and distinct microbiome characteristics.MethodsAn observational, cross-sectional study was conducted at the bronchiectasis programme of the Policlinico Hospital in Milan, Italy, where adults with bronchiectasis were enrolled between March 2017 and March 2019. Active neutrophil elastase was measured on sputum collected during stable state, microbiota analysed through 16S rRNA gene sequencing, molecular assessment of respiratory pathogens carried out through real-time PCR and clinical data collected.ResultsAmong 185 patients enrolled, decreasing α-diversity, evaluated through the Shannon entropy (ρ −0.37, p<0.00001) and Pielou's evenness (ρ −0.36, p<0.00001) and richness (ρ −0.33, p<0.00001), was significantly correlated with increasing elastase. A significant difference in median levels of Shannon entropy as detected between patients with neutrophil elastase ≥20 µg·mL−1 (median 3.82, interquartile range 2.20–4.96) versus neutrophil elastase <20 µg·mL−1 (4.88, 3.68–5.80; p<0.0001). A distinct microbiome was found in these two groups, mainly characterised by enrichment with Pseudomonas in the high-elastase group and with Streptococcus in the low-elastase group. Further confirmation of the association of Pseudomonas aeruginosa with elevated active neutrophil elastase was found based on standard culture and targeted real-time PCR.ConclusionsHigh levels of active neutrophil elastase are associated to low microbiome diversity and specifically to P. aeruginosa infection.

scholarly journals The Depth-Depended Fungal Diversity and Non-depth-Depended Aroma Profiles of Pit Mud for Strong-Flavor Baijiu

2022 ◽  
Vol 12 ◽  
Author(s):  
Wenchao Cai ◽  
Yu’ang Xue ◽  
Fengxian Tang ◽  
Yurong Wang ◽  
Shaoyong Yang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Essential Factor ◽  
Total Acid ◽  
Spatial Distribution Characteristics ◽  
Physicochemical Factors ◽  
Pit Mud ◽  
Different Depths ◽  
Electronic Nose Technology

Microorganisms in pit mud are the essential factor determining the style of strong flavor Baijiu. The spatial distribution characteristics of fungal communities and aroma in the pit mud for strong flavor Baijiu from Xinjiang, China, were investigated using Illumina MiSeq high-throughput sequencing and electronic nose technology. A total of 138 fungal genera affiliated with 10 fungal phyla were identified from 27 pit mud samples; of these, Saccharomycopsis, Aspergillus, and Apiotrichum were the core fungal communities, and Aspergillus and Apiotrichum were the hubs that maintain the structural stability of fungal communities in pit mud. The fungal richness and diversity, as well as aroma of pit mud, showed no significant spatial heterogeneity, but divergences in pit mud at different depths were mainly in pH, total acid, and high abundance fungi. Moisture, NH4+, and lactate were the main physicochemical factors involved in the maintenance of fungal stability and quality in pit mud, whereas pH had only a weak effect on fungi in pit mud. In addition, the fungal communities of pit mud were not significantly associated with the aroma. The results of this study provide a foundation for exploring the functional microorganisms and dissecting the brewing mechanism of strong flavor Baijiu in Xinjiang, and also contributes to the improvement of pit mud quality by bioaugmentation and controlling environmental physicochemical factors.

scholarly journals Control of Streptomyces alfalfae XY25T Over Clubroot Disease and Its Effect on Rhizosphere Microbial Community in Chinese Cabbage Field Trials

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuanliang Hu ◽  
Lu Qiu ◽  
Zongjie Zhang ◽  
Kai Liu ◽  
Xian Xia ◽  
...  
Keyword(s):  
Microbial Community ◽  
Chinese Cabbage ◽  
Field Experiments ◽  
Available Phosphorus ◽  
Sequencing Analysis ◽  
Clubroot Disease ◽  
Great Ability ◽  
Bacterial Phyla ◽  
Significant Difference ◽  
Rhizosphere Microbial Community

Clubroot caused by Plasmodiophora brassicae is one of the most destructive diseases in cruciferous crops. Streptomyces alfalfae XY25T, a biological control agent, exhibited great ability to relieve clubroot disease, regulate rhizosphere bacterial and fungal communities in Chinese cabbage, and promote its growth in greenhouse. Therefore, field experiments were carried out to investigate the effects of S. alfalfae XY25T on clubroot and rhizosphere microbial community in Chinese cabbage. Results showed that the control efficiency of clubroot by S. alfalfae XY25T was 69.4%. Applying the agent can alleviate soil acidification; increase the contents of soil organic matter, available nitrogen, available phosphorus, and available potassium; and enhance activities of invertase, urease, catalase, and alkaline phosphatase. During Chinese cabbage growth, bacterial diversity decreased first and then increased, and fungal diversity decreased gradually after inoculation with S. alfalfae XY25T. High-throughput sequencing analysis showed that the main bacterial phyla were Proteobacteria, Bacteroidetes, Acidobacteria, and Planctomycetes, and the major fungal phyla were Ascomycota and Basidiomycota in rhizosphere soil. The dominant bacterial genera were Flavobacterium, Candidatus, Pseudomonas, Stenotrophomonas, Sphingomonas, Flavisolibacter, and Gemmatimonbacteria with no significant difference in abundance, and the major fungal genera were Monographella, Aspergillus, Hypocreales, Chytridiaceae, Fusarium, Pleosporales, Agaricales, Mortierella, and Pleosporales. The significant differences were observed among Pleosporales, Basidiomycota, Colletotrichum, two strains attributed to Agaricales, and another two unidentified fungi by using S. alfalfae XY25T. Moreover, quantitative real-time PCR results indicated that P. brassicae content was significantly decreased after the agent inoculation. In conclusion, S. alfalfae XY25T can affect rhizosphere microbial communities; therefore, applying the agent is an effective approach to reduce the damage caused by clubroot.

scholarly journals Fresh Rumen Liquid Inoculant Enhances the Rumen Microbial Community Establishment in Pre-weaned Dairy Calves

2022 ◽  
Vol 12 ◽  
Author(s):  
Hanna Huuki ◽  
Seppo Ahvenjärvi ◽  
Paula Lidauer ◽  
Milka Popova ◽  
Johanna Vilkki ◽  
...  
Keyword(s):  
Weight Gain ◽  
Microbial Community ◽  
Microbial Community Composition ◽  
Operational Taxonomic Unit ◽  
Monozygotic Twin ◽  
Rrna Gene ◽  
Rumen Microorganisms ◽  
Significant Difference ◽  
Archaeal Communities ◽  
Ciliate Protozoa

The development of the functional rumen in calves involves a complex interplay between the host and host-related microbiome. Attempts to modulate rumen microbial community establishment may therefore have an impact on weaning success, calf health, and animal performance later in life. In this experiment, we aimed to elucidate how rumen liquid inoculum from an adult cow, provided to calves during the pre-weaning period, influences the establishment of rumen bacterial, archaeal, fungal, and ciliate protozoan communities in monozygotic twin calves (n = 6 pairs). The calves were divided into treatment (T-group) and control (C-group) groups, where the T-group received fresh rumen liquid as an oral inoculum during a 2–8-week period. The C-group was not inoculated. The rumen microbial community composition was determined using bacterial and archaeal 16S ribosomal RNA (rRNA) gene, protozoal 18S rRNA gene, and fungal ITS1 region amplicon sequencing. Animal weight gain and feed intake were monitored throughout the experiment. The T-group tended to have a higher concentrate intake (Treatment: p &lt; 0.08) and had a significantly higher weekly weight gain (Treatment: p &lt; 0.05), but no significant difference in volatile fatty acid concentrations between the groups was observed. In the T-group, the inoculum stimulated the earlier establishment of mature rumen-related bacterial taxa, affecting significant differences between the groups until 6 weeks of age. The inoculum also increased the archaeal operational taxonomic unit (OTU) diversity (Treatment: p &lt; 0.05) but did not affect the archaeal quantity. Archaeal communities differed significantly between groups until week 4 (p = 0.02). Due to the inoculum, ciliate protozoa were detected in the T-group in week 2, while the C-group remained defaunated until 6 weeks of age. In week 8, Eremoplastron dilobum was the dominant ciliate protozoa in the C-group and Isotricha sp. in the T-group, respectively. The Shannon diversity of rumen anaerobic fungi reduced with age (Week: p &lt; 0.01), and community establishment was influenced by a change of diet and potential interaction with other rumen microorganisms. Our results indicate that an adult cow rumen liquid inoculum enhanced the maturation of bacterial and archaeal communities in pre-weaning calves’ rumen, whereas its effect on eukaryotic communities was less clear and requires further investigation.

scholarly journals The Value of Vaginal Microbiome in Patients with Endometrial Hyperplasia

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Hu Zhang ◽  
Qiao Feng ◽  
Zhanpeng Zhu ◽  
Haiyan Dai ◽  
Hua Hu
Keyword(s):  
Endometrial Hyperplasia ◽  
Abnormal Uterine Bleeding ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Bacterial Populations ◽  
Α Diversity ◽  
Significant Difference ◽  
Proliferative Endometrium ◽  
Microbial Dna ◽  
Insight Into

Objective. To investigate the profiles of the vaginal microbiome in patients with endometrial hyperplasia and to explore the potential value of vaginal microbiome in the diagnosis of endometrial hyperplasia. Materials/Methods. 26 patients suffering from abnormal uterine bleeding (AUB) with thickened endometrium revealed by transvaginal ultrasonography were enrolled. Based on pathology, 12 patients with endometrial hyperplasia were classified as the Veh group and 14 patients with proliferative endometrium were classified as the Vne group. The vaginal samples were collected for the presence of microbial DNA by high-throughput next-generation sequencing of the 16S rRNA gene. The α-diversity and ß-diversity of vaginal microbiome were analyzed and compared between bacterial populations. The ROC curve was made to evaluate the feasibility of flora as a biomarker. Results. The diversity of vaginal microbiome in the Veh group was significantly lower than that in the Vne group ( P < 0.05 ). Lactobacillus was the most represented genus in the Veh group. The study’s t-test between the two groups showed that Lactobacillus has the only significant difference in the abundance of the first 15 genera ( P < 0.01 ). ROC analysis of the abundance of Lactobacillus showed that the area of AUC was 0.83, the sensitivity was 93.00%, and the specificity was 75.00%. Conclusion. The study offers insight into the nature of the vaginal microbiome and suggests that surveying the vaginal microbiota might be useful for detection of endometrial hyperplasia.

scholarly journals Changes in Microbial Community Structures under Reclaimed Water Replenishment Conditions

2020 ◽  
Vol 17 (4) ◽  
pp. 1174
Author(s):  
Jie Li ◽  
Yujiao Sun ◽  
Xiaoyu Wang ◽  
Shangwei Xu
Keyword(s):  
Microbial Community ◽  
Water Resources ◽  
Natural Water ◽  
Water Environment ◽  
Reclaimed Water ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Community Structures ◽  
Significant Difference ◽  
Microbial Community Structures

Using reclaimed water as a resource for landscape water replenishment may alleviate the major problems of water resource shortages and water environment pollution. However, the safety of the reclaimed water and the risk of eutrophication caused by the reclaimed water replenishment are unclear to the public and to the research community. This study aimed to reveal the differences between natural water and reclaimed water and to discuss the rationality of reclaimed water replenishment from the perspective of microorganisms. The microbial community structures in natural water, reclaimed water and natural biofilms were analyzed, and the community succession was clarified along the ecological niches, water resources, fluidity and time using 16S rRNA gene amplicon sequencing. Primary biofilms without the original community were added to study the formation of microbial community structures under reclaimed water acclimation. The results showed that the difference caused by ecological niches was more than those caused by the fluidity of water and different water resources. No significant difference caused by the addition of reclaimed water was found in the microbial diversity and community structure. Based on the results of microbial analysis, reclaimed water replenishment is a feasible solution that can be used for supplying river water.

scholarly journals A Pilot Study on the Microbiome of Amblyomma hebraeum Tick Stages Infected and Non-Infected with Rickettsia africae

Pathogens ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 941
Author(s):  
Dalicia Kisten ◽  
Jory Brinkerhoff ◽  
Selaelo Ivy Tshilwane ◽  
Samson Mukaratirwa
Keyword(s):  
Microbial Community ◽  
Pilot Study ◽  
Microbial Community Composition ◽  
Blood Feeding ◽  
Rrna Gene ◽  
Eastern Cape ◽  
Amblyomma Hebraeum ◽  
Rickettsia Africae ◽  
Significant Difference ◽  
Single Genus

Variation in tick microbiota may affect pathogen acquisition and transmission but for many vector species, including Amblyomma hebraeum, components and determinants of the microbiome are unidentified. This pilot study aimed to determine baseline microbial community within A. hebraeum nymphs infected- and non-infected with Rickettsia africae from the environment, and within adult ticks infected- and non-infected with R. africae collected from cattle sampled from two locations in the Eastern Cape province of South Africa. Adult A. hebraeum ticks (N = 13) and A. hebraeum nymph (N = 15) preliminary screened for R. africae were randomly selected and subjected to Illumina sequencing targeting the v3–v4 hypervariable regions of the 16S rRNA gene. No significant difference in microbial community composition, as well as rarefied OTU richness and diversity were detected between adults and nymphs. Nymphs showed a higher richness of bacterial taxa indicating blood-feeding could have resulted in loss of microbial diversity during the moulting stage from nymph to adult. Core OTUs that were in at least 50% of nymphs and adults negative and positive for Rickettsia at 1% minimum relative abundance were Rickettsia, Coxiella and Ruminococcaceae UCG-005 with a single genus Arsenophonus occurring only in nymphs negative for Rickettsia. Ehrlichia spp. was present in only four nymphal ticks positive for Rickettsia. Interestingly, Rickettsia aeschlimannii was found in one nymph and one adult, indicating the first ever detection of the species in A. hebraeum. Furthermore, A. hebraeum harboured a Coxiella-like endosymbiont, which should be investigated further as Coxiella may affect the viability and transmission of other organisms.

scholarly journals Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Zhang ◽  
Qingsong Yang ◽  
Juan Ling ◽  
Lijuan Long ◽  
Hui Huang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
16S Rrna Gene Sequencing ◽  
Physiological Status ◽  
Rrna Gene ◽  
Coral Host ◽  
Pocillopora Damicornis ◽  
Coral Microbiome ◽  
Α Diversity

Abstract Background The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the ability of this host to cope with complex and changing marine environments. In this study, the coral Pocillopora damicornis was inoculated with a beneficial microorganisms for corals (BMC) consortium to investigate how the coral host and its associated microbial community would respond. Results High-throughput 16S rRNA gene sequencing revealed no significant differences in bacterial community α-diversity. However, the bacterial community structure differed significantly between the BMC and placebo groups at the end of the experiment. Addition of the BMC consortium significantly increased the relative abundance of potentially beneficial bacteria, including the genera Mameliella and Endozoicomonas. Energy reserves and calcification rates of the coral host were also improved by the addition of the BMC consortium. Co-occurrence network analysis indicated that inoculation of coral with the exogenous BMC consortium improved the physiological status of the host by shifting the coral-associated microbial community structure. Conclusions Manipulating the coral-associated microbial community may enhance the physiology of coral in normal aquarium conditions (no stress applied), which may hypothetically contribute to resilience and resistance in this host.

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