scholarly journals Monitoring the Antibacterial Effect of Rosin Acids in an Austrian Beet Sugar Plant by Amplicon-Based Sequencing and Flow Cytometry

2021 ◽  
Vol 11 (2) ◽  
pp. 737
Author(s):  
Cordula K. Moser ◽  
Christina Ukowitz ◽  
Ulrike Zitz ◽  
Florian Emerstorfer ◽  
Walter Hein ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Rosin Acid ◽  
Thermophilic Bacteria ◽  
Antimicrobial Effect ◽  
Illumina Miseq ◽  
Process Conditions ◽  
Extraction Area ◽  
Beet Sugar ◽  
Bacillus Spp ◽  
Sugar Plant

For decades, microorganisms in beet sugar production have been studied using culture-based methods. However, these methods are not sufficient to describe such a complex bacterial community. In this study, therefore, an amplicon-based sequencing technique (Illumina MiSeq platform) was applied to characterize the bacterial community and its dynamics in the extraction area and juice purification station of an Austrian beet sugar plant. Depending on the process conditions thermophilic bacteria, such as Geobacillus spp., Caenibacillus spp., and Thermus spp., and mesophilic bacteria, such as Leuconostoc spp. and Bacillus spp., were found. Besides these microbiological characteristics, the antimicrobial effect of a rosin acid-based product (Defostab 220) on the bacterial communities was investigated in industrial and laboratory trials. The antimicrobial effect of a given concentration of rosin acid varies from bacteriostatic to bactericidal effects on different occurring groups of bacteria.

scholarly journals Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 569
Author(s):  
Chakriya Sansupa ◽  
Sara Fareed Mohamed Wahdan ◽  
Terd Disayathanoowat ◽  
Witoon Purahong
Keyword(s):  
Bacterial Community ◽  
Forest Soil ◽  
Culture Media ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Enrichment Cultures ◽  
Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

Analysis of the effects of nanosilver on bacterial community in the intestinal fluid of silkworms using high-throughput sequencing

2019 ◽  
Vol 110 (3) ◽  
pp. 309-320
Author(s):  
Chen Lin ◽  
Zhou Wei ◽  
Zhou Yi ◽  
Tan Tingting ◽  
Du Huamao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Intestinal Bacteria ◽  
Illumina Miseq ◽  
The Body ◽  
Dependent Manner ◽  
Negative Effects ◽  
Silkworm Larvae ◽  
Intestinal Bacterial Community

AbstractNanosilver is an environment-friendly, harmless alternative of traditional disinfectants which can be potentially applied in the sericulture industry. However, the effects of nanosilver on the intestinal bacterial community of the silkworms (Bombyx mori L.) are unclear. In this study, Illumina MiSeq high-throughput sequencing technology was used to assess the intestinal bacterial community in both male and female silkworms while treated with different concentrations of nanosilver. We found that nanosilver significantly influenced the composition of silkworm intestinal bacterial community on the different taxonomic levels. Most conspicuously, the abundance of Firmicutes was increased by the treatment of 20 mg L−1 nanosilver but decreased by that of 100 mg L−1 nanosilver at the phylum level. The same trend was observed in Bacilli at the class level and in Enterococcus at the genus level. In some extreme cases, application of nanosilver eliminated the bacterium, e.g., Brevibacillus, but increased the population of several other bacteria in the host intestine, such as Blautia, Terrisporobacter, Faecalibacterium, and some bacteria could only be found in nanosilver treatment groups, e.g., Dialister. In addition, although nanosilver generally showed negative effects on the cocooning rate in a dose-dependent manner, we found that 20 mg L−1 nanosilver treatment significantly increased the body weight of silkworms and did not show negative effects on the survival rate. These results indicated that the intestinal bacteria community of silkworm larvae was significantly changed after nanosilver treatment which might consequently influence host growth and development.

scholarly journals Exploring possible associations of the intestine bacterial microbiome with the pre-weaned weight gaining performance of piglets in intensive pig production

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xinghua Ding ◽  
Wensheng Lan ◽  
Gang Liu ◽  
Hengjia Ni ◽  
Ji-Dong Gu
Keyword(s):  
Weight Gain ◽  
Bacterial Community ◽  
16S Rrna ◽  
Illumina Miseq ◽  
Microbial Interactions ◽  
Intestinal Microbiome ◽  
Weaned Piglets ◽  
Pig Production ◽  
Host Health ◽  
Bacterial Microbiome

Abstract The pre-weaned weight gain is an important performance trait of pigs in intensive pig production. The bacterial microbiome inside the host is vital to host health and growth performance. The purpose of this study was to explore the possible associations of the intestinal microbiome with the pre-weaned weight gain in intensive pig production. In this study, several anatomical sites (jejunum, ileum, cecum, and colon) were examined for bacterial microbiome structure using 16S rRNA V4-V5 region sequencing with Illumina Miseq. The results showed that the microbial richness (estimated by Chao1 index) in jejunum was positively correlated with the pre-weaned weight gain. This study also revealed that the Firmicutes and Bacteroidetes in colon were the weight gaining-related phyla; while the Selenomonas and Moraxella in ileum and the Lactobacillus in both cecum and colon were the weight gaining-related genera for the pre-weaned piglets in intensive pig prodution. Several intra-microbial interactions within commensal microbiome correlated with the pre-weaned weight gain were excavated, as well. Overall, this study provides an expanded view of the commensal bacterial community inside four anatomical intestinal sites of the commercial piglets and the associations of the intestinal microbiome with the pre-weaned weight gaining performance in intensive pig production.

scholarly journals A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Siwen Deng ◽  
Heidi M.-L. Wipf ◽  
Grady Pierroz ◽  
Ted K. Raab ◽  
Rajnish Khanna ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Amendment ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Microbiome ◽  
Plant Growth Promoting ◽  
Miseq Platform ◽  
Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

scholarly journals Bacterial Community Structure of Pinus Thunbergii Naturally Infected by the Nematode Bursaphelenchus Xylophilus

2020 ◽  
Vol 8 (2) ◽  
pp. 307 ◽  
Author(s):  
Yang Ma ◽  
Zhao-Lei Qu ◽  
Bing Liu ◽  
Jia-Jin Tan ◽  
Fred O. Asiegbu ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Pine Wilt Disease ◽  
Illumina Miseq ◽  
Bursaphelenchus Xylophilus ◽  
Functional Structure ◽  
Genetic Information Processing ◽  
The Difference ◽  
And Function

Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p < 0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.

scholarly journals The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection

Gut ◽  
2016 ◽  
Vol 67 (2) ◽  
pp. 216-225 ◽  
Author(s):  
Christian Schulz ◽  
Kerstin Schütte ◽  
Nadine Koch ◽  
Ramiro Vilchez-Vargas ◽  
Melissa L Wos-Oxley ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Illumina Miseq ◽  
Gi Tract ◽  
Upper Gi ◽  
Miseq Platform ◽  
H Pylori ◽  
Bacterial Assemblages ◽  
First Time ◽  
Upper Gi Tract

ObjectivePatients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches.DesignSaliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52.2±SD 14.5 years). RNA was extracted and the V1–V2 region of the retrotranscribed bacterial 16S rRNA amplified and sequenced on the Illumina MiSeq platform.ResultsOverall, 687 bacterial phylotypes that belonged to 95 genera and 11 phyla were observed. Each individual comprised a unique microbiota composition that was consistent across the different niches. However, the stomach fluid enriched for specific microbiota components. Helicobacter spp were shown to dominate the mucosa-associated community in the stomach, and to significantly influence duodenal and oral communities.ConclusionsThe detailed analysis of the active global bacterial communities from the five distinct sites of the upper GI tract allowed for the first time the differentiation between host effects and the influence of sampling region on the bacterial community. The influence of Helicobacter spp on the global community structures is striking.

scholarly journals Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

2014 ◽  
Vol 81 (4) ◽  
pp. 1530-1539 ◽  
Author(s):  
Merete Wiken Dees ◽  
Erik Lysøe ◽  
Berit Nordskog ◽  
May Bente Brurberg
Keyword(s):  
Bacterial Community ◽  
Pathogenic Bacteria ◽  
Bacterial Colonization ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Human Pathogens ◽  
Content Type ◽  
Leaf Maturity ◽  
Leafy Greens ◽  
Over Time

ABSTRACTThe phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of theL. sativasamples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied betweenD. tenuifoliaandL. sativaat harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development.

scholarly journals Comparison of the bacterial abundance and diversity in the Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) between both sexes

2019 ◽  
Author(s):  
Chunhui Guo ◽  
Xin Peng ◽  
Xialin Zheng ◽  
Xiaoyun Wang ◽  
Ruirui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Illumina Miseq ◽  
Invasive Pest ◽  
Operational Taxonomic Units ◽  
Adult Females ◽  
Comprehensive Comparison ◽  
Leptocybe Invasa ◽  
Sex Regulation ◽  
Abundance And Diversity ◽  
Dominant Bacteria

Background. Insects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and both female-biased sex ratios and thelytokous parthenogenesis in L. invasa contribute to the rapid invasion and fast growth of the population. However, the interior bacterial composition and abundance of L. invasa and the differences between both sexes remain unclear. Results. The Illumina MiSeq platform was used to compare the composition of the bacterial community in adult females and males by sequencing with variation in the V3-V4 region of the 16S ribosomal DNA gene. The results showed that 1320 operational taxonomic units (OTUs) were obtained in total. These OTUs were annotated into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males was Rickettsia and Rhizobium, respectively. Conclusion. The bacteria living in L. invasa adult females and males had high diversity. There were differences in the bacterial community in L. invasa between both sexes, and the bacterial diversity in male adults was more abundant than that in female adults. This study presents a comprehensive comparison of bacterial communities living in L. invasa between sexes, which plays a significant role in reproductive strategy, sex regulation and the invasive mechanism of L. invasa and provides a basis for follow-up studies on the coevolution and interaction between L. invasa and its predominant bacteria.

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