scholarly journals Caterpillars lack a resident gut microbiome

2017 ◽  
Vol 114 (36) ◽  
pp. 9641-9646 ◽  
Author(s):  
Tobin J. Hammer ◽  
Daniel H. Janzen ◽  
Winnie Hallwachs ◽  
Samuel P. Jaffe ◽  
Noah Fierer
Keyword(s):  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Ecological Interactions ◽  
Agricultural Pests ◽  
Evolutionary Diversification ◽  
Transit Times ◽  
Microbial Symbionts ◽  
Rrna Gene Sequencing

Many animals are inhabited by microbial symbionts that influence their hosts’ development, physiology, ecological interactions, and evolutionary diversification. However, firm evidence for the existence and functional importance of resident microbiomes in larval Lepidoptera (caterpillars) is lacking, despite the fact that these insects are enormously diverse, major agricultural pests, and dominant herbivores in many ecosystems. Using 16S rRNA gene sequencing and quantitative PCR, we characterized the gut microbiomes of wild leaf-feeding caterpillars in the United States and Costa Rica, representing 124 species from 15 families. Compared with other insects and vertebrates assayed using the same methods, the microbes that we detected in caterpillar guts were unusually low-density and variable among individuals. Furthermore, the abundance and composition of leaf-associated microbes were reflected in the feces of caterpillars consuming the same plants. Thus, microbes ingested with food are present (although possibly dead or dormant) in the caterpillar gut, but host-specific, resident symbionts are largely absent. To test whether transient microbes might still contribute to feeding and development, we conducted an experiment on field-collected caterpillars of the model speciesManduca sexta. Antibiotic suppression of gut bacterial activity did not significantly affect caterpillar weight gain, development, or survival. The high pH, simple gut structure, and fast transit times that typify caterpillar digestive physiology may prevent microbial colonization. Moreover, host-encoded digestive and detoxification mechanisms likely render microbes unnecessary for caterpillar herbivory. Caterpillars illustrate the potential ecological and evolutionary benefits of independence from symbionts, a lifestyle that may be widespread among animals.

scholarly journals Caterpillars lack a resident gut microbiome

2017 ◽  
Author(s):  
Tobin J. Hammer ◽  
Daniel H. Janzen ◽  
Winnifred Hallwachs ◽  
Samuel L. Jaffe ◽  
Noah Fierer
Keyword(s):  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Ecological Interactions ◽  
Agricultural Pests ◽  
Evolutionary Diversification ◽  
Transit Times ◽  
Microbial Symbionts ◽  
Rrna Gene Sequencing

AbstractMany animals are inhabited by microbial symbionts that influence their hosts’ development, physiology, ecological interactions, and evolutionary diversification. However, firm evidence for the existence and functional importance of resident microbiomes in larval Lepidoptera (caterpillars) is lacking, despite the fact that these insects are enormously diverse, major agricultural pests, and dominant herbivores in many ecosystems. Using 16S rRNA gene sequencing and quantitative PCR, we characterized the gut microbiomes of wild leaf-feeding caterpillars in the United States and Costa Rica, representing 124 species from 16 families. Compared with other insects and vertebrates assayed using the same methods, the microbes we detected in caterpillar guts were unusually low-density and highly variable among individuals. Furthermore, the abundance and composition of leaf-associated microbes were reflected in the feces of caterpillars consuming the same plants. Thus, microbes ingested with food are present (though possibly dead or dormant) in the caterpillar gut, but host-specific, resident symbionts are largely absent. To test whether transient microbes might still contribute to feeding and development, we conducted an experiment on field-collected caterpillars of the model speciesManduca sexta. Antibiotic suppression of gut bacterial activity did not significantly affect caterpillar weight gain, development, or survival. The high pH, simple gut structure, and fast transit times that typify caterpillar digestive physiology may prevent microbial colonization. Moreover, host-encoded digestive and detoxification mechanisms likely render microbes unnecessary for caterpillar herbivory. Caterpillars illustrate the potential ecological and evolutionary benefits of independence from symbionts, a lifestyle which may be widespread among animals.

scholarly journals Fetal gut colonization: meconium does not have a detectable microbiota before birth

2021 ◽  
Author(s):  
Katherine M. Kennedy ◽  
Max J. Gerlach ◽  
Thomas Adam ◽  
Markus M. Heimesaat ◽  
Laura Rossi ◽  
...  
Keyword(s):  
Positive Culture ◽  
16S Rrna Gene Sequencing ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Gut Colonization ◽  
First Pass ◽  
Rrna Gene Sequencing ◽  
Negative Controls ◽  
Host Metabolism

AbstractMicrobial colonization of the human intestine impacts host metabolism and immunity, however when colonization occurs is unclear. Although numerous studies have reported bacterial DNA in first-pass meconium samples, these samples are collected hours to days after birth. We investigated whether bacteria could be detected in meconium prior to birth. Fetal meconium (n = 20) was collected by rectal swab during elective breech Cesarean sections without labour prior to antibiotics and compared to technical and procedural controls (n = 5), first-pass meconium (neonatal meconium; n = 14), and infant stool (n = 25). Unlike first-pass meconium, no microbial signal distinct from negative controls was detected in fetal meconium by 16S rRNA gene sequencing. Additionally, positive aerobic (n = 10 of 20) and anaerobic (n = 12 of 20) clinical cultures of fetal meconium (13 of 20 samples positive in at least one culture) were identified as likely skin contaminants, most frequently Staphylococcus epidermidis, and not detected by sequencing in most samples (same genera detected by culture and sequencing in 2 of 13 samples with positive culture). We conclude that fetal gut colonization does not occur before birth, and that microbial profiles of neonatal meconium reflect populations acquired during and after birth.

scholarly journals Bacterial communities associated with cell phones and shoes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9235
Author(s):  
David A. Coil ◽  
Russell Y. Neches ◽  
Jenna M. Lang ◽  
Guillaume Jospin ◽  
Wendy E. Brown ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Phones ◽  
Human Microbiome ◽  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Sporting Events ◽  
Rrna Gene Sequencing ◽  
Source And Sink

Background Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings We report here a large-scale study of the microbiome found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiome, while shoes can act as sampling devices for microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiome of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions We place this data in the context of previous studies and demonstrate that the microbiome of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.

scholarly journals Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ryan R. Cook ◽  
Jennifer A. Fulcher ◽  
Nicole H. Tobin ◽  
Fan Li ◽  
David J. Lee ◽  
...  
Keyword(s):  
Public Health Problem ◽  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Rrna Gene ◽  
People Living With Hiv ◽  
Major Public Health Problem ◽  
Microbiome Composition ◽  
Rrna Gene Sequencing ◽  
Sex With Men ◽  
Living With Hiv

Abstract Methamphetamine (MA) use is a major public health problem in the United States, especially among people living with HIV (PLWH). Many MA-induced neurotoxic effects are mediated by inflammation and gut microbiota may play a role in this process, yet the effects of MA on the microbiome have not been adequately explored. Therefore, we performed 16S rRNA gene sequencing on rectal swab samples from 381 men who have sex with men, 48% of whom were PLWH and 41% of whom used MA. We compared microbiome composition between MA users and non-users while testing for potential interactions with HIV and controlling for numerous confounders using inverse probability of treatment weighting. We found that MA use explained significant variation in overall composition (R2 = 0.005, p = 0.008) and was associated with elevated Finegoldia, Parvimonas, Peptoniphilus, and Porphyromonas and reduced Butyricicoccus and Faecalibacterium, among others. Genera including Actinomyces and Streptobacillus interacted with HIV status, such that they were increased in HIV+ MA users. Finegoldia and Peptoniphilus increased with increasing frequency of MA use, among others. In summary, MA use was associated with a microbial imbalance favoring pro-inflammatory bacteria, including some with neuroactive potential and others that have previously been associated with poor HIV outcomes.

scholarly journals Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7548 ◽  
Author(s):  
Carl J. Yeoman ◽  
Laura M. Brutscher ◽  
Özcan C. Esen ◽  
Furkan Ibaoglu ◽  
Curtis Fowler ◽  
...  
Keyword(s):  
Control Strategies ◽  
Draft Genome ◽  
Wheat Yield ◽  
Natural Populations ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Agricultural Pests ◽  
Wheat Stem Sawfly ◽  
Cephus Cinctus ◽  
Microbial Symbionts

Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies.

scholarly journals Bacterial communities associated with cell phones and shoes

2019 ◽  
Author(s):  
David A Coil ◽  
Russell Y Neches ◽  
Jenna M Lang ◽  
Guillaume Jospin ◽  
Wendy E Brown ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Phones ◽  
Human Microbiome ◽  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Sporting Events ◽  
Rrna Gene Sequencing ◽  
Source And Sink

Background: Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings: We report here a large-scale study of the microbiota found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiota, while shoes can act as sampling devices for the microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiota of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions: We place this data in the context of previous studies and demonstrate that the microbiota of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.

scholarly journals Bacterial communities associated with cell phones and shoes

2019 ◽  
Author(s):  
David A Coil ◽  
Russell Y Neches ◽  
Jenna M Lang ◽  
Guillaume Jospin ◽  
Wendy E Brown ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Phones ◽  
Human Microbiome ◽  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Sporting Events ◽  
Rrna Gene Sequencing ◽  
Source And Sink

Background: Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. Therefore, the microbiome of personal accessories are of interest because they serve as both a microbial source and sink for an individual, they may provide information about the microbial exposure experienced by an individual, and they can be sampled non-invasively. Findings: We report here a large-scale study of the microbiota found on cell phones and shoes. Cell phones serve as a potential source and sink for skin and oral microbiota, while shoes can act as sampling devices for the microbial environmental experience. Using 16S rRNA gene sequencing, we characterized the microbiota of thousands of paired sets of cell phones and shoes from individuals at sporting events, museums, and other venues around the United States. Conclusions: We place this data in the context of previous studies and demonstrate that the microbiota of phones and shoes are different. This difference is driven largely by the presence of “environmental” taxa (taxa from groups that tend to be found in places like soil) on shoes and human-associated taxa (taxa from groups that are abundant in the human microbiome) on phones. This large dataset also contains many novel taxa, highlighting the fact that much of microbial diversity remains uncharacterized, even on commonplace objects.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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