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 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 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 Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
César Ruiz ◽  
Marcela Villegas-Plazas ◽  
Olivier P Thomas ◽  
Howard Junca ◽  
Thierry Pérez
Keyword(s):  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Sponge Species ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
16S Amplicon Sequencing ◽  
Ecological Success ◽  
Specific Community ◽  
First Time ◽  
The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

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 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 16S rRNA Amplicon Sequencing of Bagworm Metisa plana Walker (Lepidoptera: Psychidae)

2021 ◽  
Author(s):  
Andrew Chung Jie Ting ◽  
Cik Mohd Rizuan ZAINAL ABIDIN ◽  
Noor Hisham HAMID ◽  
Ghows Azzam ◽  
Hasber Salim
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Amplicon Sequencing ◽  
16S Rrna Amplicon Sequencing ◽  
Outbreak Area ◽  
The Family ◽  
Family Level ◽  
Late Instar ◽  
Early Instar

The bagworm Metisa plana is one of the major pests in the oil palm plantation in Malaysia, with infestation that results in huge economical loss. Currently, the exact cause of the infestation is still undetermined. Studying the bacterial community of M. plana could provide insight on the problem as the bacteria associated with insects often provide numerous benefits to the insect itself. Using 16S rRNA amplicon sequencing, the study was conducted to compare the composition of the bacterial communities of two larval stages (early instar stage and late instar stage) from outbreak area, as well as comparing the late instar stage larvae from non-outbreak and outbreak areas. Generally, the bacterial community was dominated by Proteobacteria and Actinobacteria phyla while the Enterobacteriaceae was found to be the dominant family. When comparing between the early and late instar stage, Proteobacteria phylum was found to be more abundant in the late instar stage (82.36%) than in the early instar stage (82.28%). At the family level, the Enterobacteriaceae was slightly more abundant in late instar stage (75.46%) than in early instar stage (75.29%). The instar stage was observed to have no significant impact on the bacterial variability and showed similar bacterial community structure. When comparing between the non-outbreak area and outbreak, Proteobacteria was significantly more abundant in the outbreak area (82.02%) than in the non-outbreak area (20.57%). However, Actinobacteria was significantly more abundant in the non-outbreak area (76.29%) than in the outbreak area (14.16%). At the family level, Enterobacteriaceae was more abundant in outbreak area (75.41%) than in non-outbreak area (11.67%). Microbacteriaceae was observed to be more abundant in the non-outbreak area (70.87%) than in the outbreak area (12.47%). Although the result showed no significant difference in bacterial variability between different areas, it the bacterial community structure was significantly different.

scholarly journals Derived ecological niches of indoor microbes are crucial for asthma symptoms in university dormitories

2020 ◽  
Author(s):  
Xi Fu ◽  
Yanling Li ◽  
Yi Meng ◽  
Qianqian Yuan ◽  
Zefei Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Personal Characteristics ◽  
Amplicon Sequencing ◽  
Outdoor Environment ◽  
Ecological Niches ◽  
Microbiome Composition ◽  
Taxa Richness ◽  
Asthma Symptoms ◽  
16S Rrna Amplicon Sequencing ◽  
Indoor Microbiome

AbstractIncreasing evidences from home environment indicate that microbiome community is associated with asthma. However, indoor microbiome composition can be highly diverse and dynamic, and thus current studies fail to produce consistent association. Chinese university dormitories are special high-density dwellings with a standard built environment and personal characteristics for occupants, which can be used to disentangle the complex interactions between microbes, environmental characteristics and asthma.Settled air dust and floor dust was collected from 87 dormitory rooms in Shanxi University. Bacterial community was characterized by 16S rRNA amplicon sequencing. Students (n = 357) were surveyed for asthma symptoms.Asthma symptoms were not associated with the overall bacterial richness, but associated with different phylogenetic classes. Taxa richness and abundance in Clostridia and Bacteroidia were positively associated with asthma (p < 0.05), and these taxa were mainly derived from human gut. Taxa richness (p < 0.1) and abundance (p < 0.05) in Alphaproteobacteria and Actinobacteria were protectively associated with asthma, and these taxa were mainly derived from outdoor environment. Building age, floor and curtain cleaning frequency shaped the overall bacterial community of air dust (p < 0.05). Frequent curtain cleaning increased the relative abundance of 10 protective genera (p < 0.05), and old buildings had mix effects to protective genera (p < 0.05).Our data shows that taxa from different phylogenetic classes and ecological niches have different health effects, indicating the importance of incorporating evolutionary and ecological concepts in revealing general patterns in the microbiome asthma association analysis.

scholarly journals Mode of delivery and weight shape the intestinal microbiome composition progression in preterm infants: results of a prospective study

2020 ◽  
Author(s):  
Fardou Heida ◽  
Elisabeth Kooi ◽  
Thi-Yen Nguyen ◽  
Jan Hulscher ◽  
Anne van Zoonen ◽  
...  
Keyword(s):  
Preterm Infants ◽  
Mode Of Delivery ◽  
Amplicon Sequencing ◽  
Intestinal Microbiome ◽  
Term Infants ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Extremely Preterm ◽  
Extremely Preterm Infants ◽  
Key Factor

Abstract Background: In preterm infants the intestinal microbiome differs markedly from term infants. However, it is unclear whether the microbiome follows infant specific maturation patterns or whether it is mainly characterized by varying states of dysbiosis. We investigated the development of the intestinal microbiome in extremely preterm infants over time by 16S rRNA amplicon sequencing. We analysed the first meconium and faecal samples from the 2 nd , 3 rd and 4 th weeks, and (clinical) metadata to identify the main factors influencing the microbiota composition development. Results: The study included 41 extremely preterm infants (gestational age 25-30 weeks; birth weight (BW) 430-990g). Birth via Caesarean section (CS) was associated with placental insufficiency during pregnancy and lower BW. In meconium and in weeks 2 and 3 an increased combined abundance of Escherichia and Bacteroides (maternal aerotolerant fecal bacteria) was associated with vaginal delivery (p=0.039, p=0.0002, p=0.034, respectively) while Staphylococcus epidermidis (skin bacterium) was associated with CS (p=0.001, p=0.0003 p=0.048, respectively). Secondly, a switch was observed from a microbiome dominated by S. epidermidis (Bacilli) towards a microbiome dominated by Enterobacteriaceae (Gammaproteobacteria, mainly represented by Klebsiella and Escherichia ), in which the stage of progression appeared to be dependent upon the current weight of the infant, irrespective of the week of sampling or the mode of birth. Conclusions: Our data shows that the mode of delivery does affect the meconium microbiome composition. It also suggests that the weight of the infant at the time of sampling is a better predictor for the stage of progression of the intestinal microbiome development/maturation than gestational/postnatal age. We hypothesize that impaired growth, for example due the effects of diminished placental function during pregnancy, is a key factor in the maturation of the intestinal microbiome in extreme premature infants.

scholarly journals Dynamic Changes in Microbiome Composition Following Mare’s Milk Intake for Prevention of Collateral Antibiotic Effect

2021 ◽  
Vol 11 ◽  
Author(s):  
Almagul Kushugulova ◽  
Ulrike Löber ◽  
Saniya Akpanova ◽  
Kairat Rysbekov ◽  
Samat Kozhakhmetov ◽  
...  
Keyword(s):  
Antibiotic Therapy ◽  
Antibiotic Treatment ◽  
Amplicon Sequencing ◽  
Recovery Phase ◽  
Taxonomic Composition ◽  
Biologically Active ◽  
Microbiome Composition ◽  
16S Rrna Amplicon Sequencing ◽  
Immune Parameters ◽  
Antibiotic Effect

IntroductionProbiotics and prebiotics are widely used for recovery of the human gut microbiome after antibiotic treatment. High antibiotic usage is especially common in children with developing microbiome. We hypothesized that dry Mare’s milk, which is rich in biologically active substances without containing live bacteria, could be used as a prebiotic in promoting microbial diversity following antibiotic treatment in children. The present pilot study aims to determine the impacts of dry Mare’s milk on the diversity of gut bacterial communities when administered during antibiotic treatment and throughout the subsequent recovery phase.MethodsSix children aged 4 to 5 years and diagnosed with bilateral bronchopneumonia were prescribed cephalosporin antibiotics. During the 60 days of the study, three children consumed dry Mare’s milk whereas the other three did not. Fecal samples were collected daily during antibiotic therapy and every 5 days after antibiotic therapy. Total DNA was isolated and taxonomic composition of gut microbiota was analyzed by 16S rRNA amplicon sequencing. To assess the immune status of the gut, stool samples were analyzed by bead-based multiplex assays.ResultsMare’s milk treatment seems to prevent the bloom of Mollicutes, while preventing the loss of Coriobacteriales. Immunological analysis of the stool reveals an effect of Mare’s milk on local immune parameters under the present conditions.

Sign in / Sign up

Export Citation Format

Share Document