scholarly journals Microbiome-related aspects of locust density-dependent phase transition

2020 ◽  
Author(s):  
Omer Lavy ◽  
Ohad Lewin-Epstein ◽  
Yonatan Bendett ◽  
Uri Gophna ◽  
Eran Gefen ◽  
...  
Keyword(s):  
Phase Transition ◽  
Old Testament ◽  
Transmission Rate ◽  
Bacterial Species ◽  
Horizontal Transmission ◽  
Amplicon Sequencing ◽  
Bacterial Composition ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Before And After

AbstractLocust plagues are an ancient phenomenon, with references going back to the Old Testament. These swarming pests are notorious for their tendency to aggregate and perform long migrations, consuming vast amounts of vegetation and decimating the cultivated fields on their path. However, when population density is low, locusts will express a solitary, cryptic, non-aggregating phenotype that is not considered as an agricultural pest. Although transition of locusts from the solitary to the gregarious phase has been well studied, the shifts in the locust microbiome composition associated with this phase-transition have yet to be addressed. Here, using 16S rRNA amplicon sequencing, we compared the bacterial composition of solitary desert locusts before and after a crowding-induced phase-transition. Our findings reveal that the microbiome is altered during the phase transition. We also show that this significant change in bacterial composition includes the acquisition of a specific bacterial species - Weissella cibaria (Firmicutes), which has been previously shown to induce aggregation in cockroaches. Our findings led us to hypothesize that the locust microbiome may play a role in inducing aggregation behavior, contributing to the formation and maintenance of a swarm. Employing a mathematical model, we demonstrate the potential evolutionary advantage of inducing aggregation under various environmental conditions; and specifically, when the aggregation-inducing microbe exhibits a relatively high horizontal transmission rate. This is a first description of a previously unknown and important aspect of locust phase transition, demonstrating that the phase shift includes a shift in the gut and integument bacterial composition.

scholarly journals Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1

2019 ◽  
Vol 97 (11) ◽  
pp. 4567-4578 ◽  
Author(s):  
Margaret D Weinroth ◽  
Jennifer N Martin ◽  
Enrique Doster ◽  
Ifigenia Geornaras ◽  
Jennifer K Parker ◽  
...  
Keyword(s):  
Liver Abscess ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Feedlot Cattle ◽  
Microbiome Composition ◽  
Soil Microbial ◽  
16S Rrna Amplicon Sequencing ◽  
Liver Abscesses ◽  
Geographical Regions ◽  
Antimicrobial Resistance Genes

Abstract Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.

scholarly journals Compositional and functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

2018 ◽  
Author(s):  
Zongfu Hu ◽  
Xi CHEN ◽  
Jie CHANG ◽  
Jianhua YU ◽  
Qing TONG ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Amplicon Sequencing ◽  
Freshwater Snail ◽  
Gonadal Development ◽  
Growth Stages ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Radix Auricularia

Widely distributed across the world, the freshwater snail Radix auricularia plays an important role in freshwater systems. In this study, gut bacterial communities of R. auricularia were characterized using 16S rRNA amplicon sequencing, then intestinal bacteria were compared at different growth stages: adult snails (AS) (with complete gonadal development) and juvenile snails (JS) (with incomplete gonadal development). We obtained 251,072 high quality sequences which were clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria and Cyanobacteria, followed by Chloroflexi, Firmicutes, and Actinobacteria. Other bacterial species such as Tenericutes, Bacteroidetes, Fusobacteria and Verrucomicrobia were present to a lesser extent. 52 bacterial families and 55 genera were found in > 1% of each sample. A large number of species could not be successfully identified. 469 core OTUs were found to make up 39.38% of all OTUs and 88.38% of all sequences. Samples obtained from juvenile organisms possessed higher ratios of Ruminococcaceae, Subdoligranulum, and Faecalibacterium than adult species. Furthermore, 16S rRNA gene data was used to predict function, showing that genes related to metabolism and environmental information processing were rich in snail samples.

scholarly journals Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate

2021 ◽  
Author(s):  
Alice Baniel ◽  
Lauren Petrullo ◽  
Arianne Mercer ◽  
Laurie Reitsema ◽  
Sierra Sams ◽  
...  
Keyword(s):  
Maternal Effects ◽  
Gut Microbiome ◽  
Early Life ◽  
Amplicon Sequencing ◽  
Microbial Colonization ◽  
Fecal Samples ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Gut Colonization ◽  
First Time

Early-life gut microbial colonization is an important process shaping host physiology, immunity and long-term health outcomes in humans and other animals. However, our understanding of this dynamic process remains poorly investigated in wild animals, where developmental mechanisms can be better understood within ecological and evolutionary relevant contexts. Using 16s rRNA amplicon sequencing on 525 fecal samples from a large cohort of infant and juvenile geladas (Theropithecus gelada), we characterized gut microbiome maturation during the first three years of life and assessed the role of maternal effects in shaping offspring microbiome assembly. Microbial diversity increased rapidly in the first months of life, followed by more gradual changes until weaning. As expected, changes in gut microbiome composition and function with increasing age reflected progressive dietary transitions: in early infancy when infants rely heavily on their mother's milk, microbes that facilitate milk glycans and lactose utilization dominated, while later in development as graminoids are progressively introduced into the diet, microbes that metabolize plant complex polysaccharides became dominant. Furthermore, the microbial community of nursing infants born to first-time (primiparous) mothers was more "milk-oriented" compared to similarly-aged infants born to experienced (multiparous) mothers. Comparisons of matched mother-offspring fecal samples to random dyads did not support vertical transmission as a conduit for these maternal effects, which instead could be explained by slower phenotypic development (and associated slower gut microbiome maturation) in infants born to first-time mothers. Together, our findings highlight the dynamic nature of gut colonization

scholarly journals Modulation of gastrointestinal bacterial in chronic atrophic gastritis model rats by Chinese and west medicine intervention

2021 ◽  
Author(s):  
Minghan Huang ◽  
Sihan Li ◽  
Youcheng He ◽  
Cuili Lin ◽  
Yueming Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Atrophic Gastritis ◽  
Close Relation ◽  
Amplicon Sequencing ◽  
Chronic Atrophic Gastritis ◽  
Bacterial Composition ◽  
Chinese Medicines ◽  
Alpha And Beta Diversity ◽  
16S Rrna Amplicon Sequencing ◽  
Pathogenic Factors

Abstract Chronic atrophic gastritis (CAG) is well-known related with multiple pathogenic factors and normally therapies comprised by western or Chinese medicines. The present study was designed to identify the bacterial community characterized by 16S rRNA amplicon sequencing and determine the modulate affection of bacterial composition response western and Chinese medicine Qinghuayin (QHY) as well as antibiotic on model rats. The result shown the overall structure alteration of bacterial appeared under medicine intervened, antibiotic caused a marked depletion in bacterial diversity and richness. The enrichments of Firmicutes (85.1-90.7%) in antibiotic-free converts into Bacteroidetes (30.7-34.6%) in antibiotic-added model rat were demonstrated. Firmicutes as the most dominant phylum in antibiotic-free treatments and significantly decreased till 21.9%-68.5% in antibiotic-added treatments. Especially QHY-treated rats showed highest RA of Firmicutes (90.7%) and the amelioration of CAG using QHY attributed by beneficial bacterial enrichment, especially Ruminococcus, Lactobacillus and Bifidobacterium. In addition, alpha and beta diversity analysis also demonstrated the clear dispersion and aggregation that revealed the alteration and steady of bacterial community structures. In summary, QHY has potential application value in the treatment of CAG, which attributed to close relation with the modulatory of internal bacterial communities.

scholarly journals Modulation of Gastrointestinal Bacterial in Chronic Atrophic Gastritis Model Rats by Chinese and West Medicine Intervention

2020 ◽  
Author(s):  
Minghan Huang ◽  
Sihan Li ◽  
Youcheng He ◽  
Cuili Lin ◽  
Yueming Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Atrophic Gastritis ◽  
Close Relation ◽  
Amplicon Sequencing ◽  
Chronic Atrophic Gastritis ◽  
Bacterial Composition ◽  
Chinese Medicines ◽  
Alpha And Beta Diversity ◽  
16S Rrna Amplicon Sequencing ◽  
Pathogenic Factors

Abstract Chronic atrophic gastritis (CAG) was well-known related with multiple pathogenic factors and normally therapies comprised by western or Chinese medicines. Present study was design to identified the bacterial community characterized by 16S rRNA amplicon sequencing and determine the modulate affection of bacterial composition response western and Chinese medicine Qing huayin (QHY) as well as antibiotic on model rats. Result shown the overall structure alteration of bacterial appeared under medicine applied, antibiotic caused a marked depletion in bacterial diversity and richness, the enrichment of Firmicutes (85.1-90.7%) in antibiotic-free convert to Bacteroidetes (30.7-34.6%) in antibiotic-added model rat were demonstrated. Firmicutes was most dominant phylum and accounting for 85.1%-90.5% and significantly decreased till 21.9%-68.5% in antibiotic-added treatments. Especially QHY-treated show highest RA of Firmicutes (90.5%) and the amelioration of CAG using QHY attributed by beneficial bacterial enrichment, especially Ruminococcus, Lactobacillus and Bifidobacterium. In addition, alpha and beta diversity analysis also demonstrated the clear dispersion and aggregation that revealed the alteration and steady of bacterial community structures. In summary, QHY has potential application value in the treatment of CAG which attributed to close relation with the modulatory of internal bacterial communities.

scholarly journals Coffee Consumption Modulates Amoxicillin-Induced Dysbiosis in the Murine Gut Microbiome

2021 ◽  
Vol 12 ◽  
Author(s):  
Emma Diamond ◽  
Katharine Hewlett ◽  
Swathi Penumutchu ◽  
Alexei Belenky ◽  
Peter Belenky
Keyword(s):  
Gut Microbiome ◽  
Burkholderia Cepacia ◽  
Coffee Consumption ◽  
Amplicon Sequencing ◽  
Antibiotic Use ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Caffeinated Coffee

The microbiome is essential for host health, and perturbations resulting from antibiotic use can lead to dysbiosis and disease. Diet can be a powerful modulator of microbiome composition and function, with the potential to mitigate the negative effects of antibiotic use. Thus, it is necessary to study the impacts of diet and drug interactions on the gut microbiome. Coffee is a commonly consumed beverage containing many compounds that have the potential to affect the microbiome, including caffeine, polyphenols, and fiber. We supplemented mice with caffeinated and decaffeinated coffee in conjunction with amoxicillin, and used 16S rRNA amplicon sequencing of fecal samples to investigate changes in diversity and composition of the murine fecal microbiome. We found that antibiotics, regardless of coffee supplementation, caused significant disruption to the murine fecal microbiome, enriching for Proteobacteria, Verrucomicrobia, and Bacteroidetes, but reducing Firmicutes. While we found that coffee alone did not have a significant impact on the composition of the fecal microbiome, coffee supplementation did significantly affect relative abundance metrics in mice treated with amoxicillin. After caffeinated coffee supplementation, mice treated with amoxicillin showed a smaller increase in Proteobacteria, specifically of the family Burkholderiaceae. Correspondingly we found that in vitro, Burkholderia cepacia was highly resistant to amoxicillin, and that it was inhibited by concentrations of caffeine and caffeinated coffee comparable to levels of caffeine in murine ceca. Overall, this work shows that coffee, and possibly the caffeine component, can impact both the microbiome and microbiome members during antibiotic exposure.

scholarly journals Comparative microbiomes of three species of laboratory-reared Periplaneta cockroaches

2019 ◽  
Author(s):  
Seogwon Lee ◽  
Ju Yeong Kim ◽  
Myung-hee Yi ◽  
In-Yong Lee ◽  
Tai-Soon Yong
Keyword(s):  
16S Rrna ◽  
Species Composition ◽  
Periplaneta Americana ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Diversity Analysis ◽  
Bacterial Composition ◽  
Microbiome Composition ◽  
Operational Taxonomic Units ◽  
Multiple Conditions

AbstractCockroaches are the most primitive insects, and are often used as the basic insect model in many studies. Three species of Periplaneta cockroaches were raised in the laboratory for many generations under the same conditions. We conducted 16S rRNA-targeted high-throughput sequencing to evaluate the overall bacterial composition in the microbiomes of three species of cockroaches. The number of operational taxonomic units (OTUs) was not significantly different between the three cockroach species. With respect to the Shannon and Pielou indexes, the microbiome of Periplaneta americana presented higher values than that of either P. japonica or P. fulginosa. In terms of species composition, endosymbionts accounted for over half of all the bacterial species in P. japonica and P. fulginosa. The beta diversity analysis showed that P. japonica and P. fulginosa exhibit a similar microbiome composition, which is different from that of P. americana. However, we also identified that P. japonica and P. fulginosa are hosts to distinct bacterial species. Thus, although the composition of the microbiome may vary based on multiple conditions, it is possible to identify distinct compositions of the microbiome among the different Periplaneta cockroach species even when individuals are reared under the same conditions.ImportanceCockroaches inhabit various habitats—which are known to be related to their microbiome—and exhibit different features depending on the species. It is expected that their microbiomes would vary according to species depending on these features. Cockroach microbiomes are known to vary based on the diet or environmental shifts. In this study, we compare the diversity of bacteria in the three cockroach species under conditions of reduced diet and environment shifts. This study can establish the basic microbiomes of three Periplaneta species and can be the basic data for cockroach research.

scholarly journals Anopheles albimanus natural microbiota is altered within one generation of laboratory colonization

2020 ◽  
Author(s):  
Nsa Dada ◽  
Ana Cristina Benedict ◽  
Francisco López ◽  
Juan C. Lol ◽  
Mili Sheth ◽  
...  
Keyword(s):  
First Generation ◽  
Amplicon Sequencing ◽  
Anopheles Albimanus ◽  
Microbiome Composition ◽  
Laboratory Conditions ◽  
16S Rrna Amplicon Sequencing ◽  
Late Instar ◽  
Microbe Interactions ◽  
First Time ◽  
Natural Microbiota

AbstractResearch on mosquito-microbe interactions may lead to new tools for mosquito and mosquito-borne disease control. To date, such research has largely utilized laboratory-reared mosquitoes that typically lack the microbial diversity of wild populations. A logical progression in this area involves working under controlled settings using field-derived mosquitoes or, in most cases, their progeny. Thus, an understanding of how laboratory colonization affects the assemblage of mosquito microbiota would aid in advancing mosquito microbiome studies and their applications beyond laboratory settings. Using high throughput 16S rRNA amplicon sequencing, we characterized the internal and cuticle surface microbiota of F1 progeny of wild-caught adult Anopheles albimanus from four locations in Guatemala. A total of 132 late instar larvae and 135 2-5day old, non-blood-fed virgin adult females that were reared under identical laboratory conditions, were pooled (3 individuals/pool) and analyzed. F1 larvae from different maternal sites showed different microbial compositions (p=0.001; F = 9.5), but these differences were absent at the adult stage (p=0.12; F =1.6). These results suggest that field-acquired mosquito microbiota may be lost in as early as the first generation of colonization under normal laboratory conditions, thus, requiring adjustments to maintain field-derived microbiota. This is the first time that the microbiota of F1 progeny of wild-caught mosquitoes has been characterized in relation to maternal collection site. Our findings provide a comprehensive background for studying how parentage and environmental conditions differentially or concomitantly affect mosquito microbiome composition, and how this can be exploited in advancing mosquito microbiome studies and their applications beyond laboratory settings.

scholarly journals Compositional and functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

2018 ◽  
Author(s):  
Zongfu Hu ◽  
Xi CHEN ◽  
Jie CHANG ◽  
Jianhua YU ◽  
Qing TONG ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Amplicon Sequencing ◽  
Freshwater Snail ◽  
Gonadal Development ◽  
Growth Stages ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Radix Auricularia

Widely distributed across the world, the freshwater snail Radix auricularia plays an important role in freshwater systems. In this study, gut bacterial communities of R. auricularia were characterized using 16S rRNA amplicon sequencing, then intestinal bacteria were compared at different growth stages: adult snails (AS) (with complete gonadal development) and juvenile snails (JS) (with incomplete gonadal development). We obtained 251,072 high quality sequences which were clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria and Cyanobacteria, followed by Chloroflexi, Firmicutes, and Actinobacteria. Other bacterial species such as Tenericutes, Bacteroidetes, Fusobacteria and Verrucomicrobia were present to a lesser extent. 52 bacterial families and 55 genera were found in > 1% of each sample. A large number of species could not be successfully identified. 469 core OTUs were found to make up 39.38% of all OTUs and 88.38% of all sequences. Samples obtained from juvenile organisms possessed higher ratios of Ruminococcaceae, Subdoligranulum, and Faecalibacterium than adult species. Furthermore, 16S rRNA gene data was used to predict function, showing that genes related to metabolism and environmental information processing were rich in snail samples.

scholarly journals Microbial Contamination Survey of Environmental Fresh and Saltwater Resources of Upolu Island, Samoa

Environments ◽  
2021 ◽  
Vol 8 (11) ◽  
pp. 112
Author(s):  
Michael A. Ochsenkühn ◽  
Cong Fei ◽  
Odmaa Bayaara ◽  
Emarosa Romeo ◽  
Patila Amosa ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Hypervariable Region ◽  
Amplicon Sequencing ◽  
Wide Distribution ◽  
Coliform Bacteria ◽  
Fecal Indicator ◽  
16S Rrna Amplicon Sequencing ◽  
Seawater Samples ◽  
Microbe Diversity

Analysis of microbe diversity in freshwater resources and nearshore seawater samples of Upolu Island was performed to investigate the distribution of harmful bacteria. For this, 124 samples were collected from 23 river systems, two volcanic lakes, and 45 locations inside and outside the barrier reef of Upolu Island, Samoa. Physicochemical parameters for general water quality, detection of coliform bacteria and 16S rRNA amplicon sequencing were performed on all samples. Fecal indicator bacteria (FIB) testing indicated a wide distribution of coliform bacteria in all sampled freshwater sites with evidence of fecal coliform in most locations. Importantly, evidence of coliform bacteria was found in most seawater samples inside and along the reef, apart from those samples taken ~20 km offshore. Illumina 16S rRNA amplicon sequencing of the V4 hypervariable region confirmed the presence of various types of harmful bacterial species, namely from the Enterobacteriaceae, Enterococcae, Streptococcaceae, and Vibrionacea families. By combining the sensitivity of FIB testing and next-generation sequencing, we were able to show the extent of potential contaminations in fresh and seawater samples and simultaneously identify the potential pathogenic bacterial genera present. The wide distribution of potential harmful bacteria from river runoff or direct sewage dumping has an impact on human health, leading to many skin and intestinal diseases, and is potentially detrimental to coral reef community health.

Sign in / Sign up

Export Citation Format

Share Document