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 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.

scholarly journals Impact of Oropharyngeal Administration of Colostrum in Preterm Newborns’ Oral Microbiome

Nutrients ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 4224
Author(s):  
Ramon V. Cortez ◽  
Andrea Fernandes ◽  
Luiz Gustavo Sparvoli ◽  
Marina Padilha ◽  
Rubens Feferbaum ◽  
...  
Keyword(s):  
Preterm Infants ◽  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Alpha And Beta Diversity ◽  
Longitudinal Observational Study ◽  
Key Factor ◽  
Rrna Gene Sequencing ◽  
Preterm Newborns

The initial colonization of the human microbiota is of paramount importance. In this context, the oropharyngeal administration of colostrum is a safe, viable, and well-tolerated practice even by the smallest preterm infants. Therefore, this study evaluated the effects of oropharyngeal administration of colostrum on the establishment of preterm infants’ oral microbiota. A longitudinal observational study was carried out with 20 premature neonates, divided into two groups: one receiving the protocol (Oropharyngeal Administration of Colostrum; OAC) and the other one receiving Standard Caare (SC). Saliva samples were collected from the newborns weekly during the study period (from the day of birth until the 21st day of life) for analysis of oral microbiota through 16S rRNA gene sequencing. We observed that the colonization of the oral microbiota of preterm newborns preseanted a higher relative abundance of Staphylococcus on the 7th day of life, mainly in the OAC group. Additionally, an increased abundance of Bifidobacterium and Bacteroides was observed in the OAC group at the first week of life. Regarding alpha and beta diversity, time was a key factor in the oral modulation of both groups, showing how dynamic this environment is in early life.

scholarly journals Tongue microbiome of smokeless tobacco users

2020 ◽  
Author(s):  
Esam Halboub ◽  
Mohammed Alakhali ◽  
Abdulwahhab H. Al-Amir ◽  
Husham E. Homeida ◽  
Divyashri Baraniya ◽  
...  
Keyword(s):  
Smokeless Tobacco ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Cross Sectional Study ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Oral Carcinogenesis ◽  
Rothia Mucilaginosa ◽  
Rrna Gene Sequencing

Abstract Background The possibility that smokeless tobacco may contribute to oral carcinogenesis by influencing the oral microbiome has not been explored. This cross sectional study sought to assess the effect of using shammah, a form of smokeless tobacco prevalent in Arabia, on the tongue microbiome. Tongue scarping samples were obtained from twenty-nine shammah users (SU; 27.34±6.9 years) and 23 shammah non-users (SNU; 27.7±7.19 years) and analyzed with 16S rRNA gene sequencing (V1-V3). Species-level taxonomy assignment of the high-quality, merged reads was obtained using a previously described BLASTn-based algorithm. Downstream analyses were performed with QIIME, LEfSe, and R. Results A total of 178 species, belonging to 62 genera and 8 phyla were identified. Genera Streptococcus , Leptotrichia , Actinomyces , Veillonella , Haemophilus , Prevotella and Neisseria accounted for more than 60% of the average microbiome. There were no differences between the two groups in species richness and alpha-diversity, but PCoA showed significant separation (P=0.015, ANOSIM). LEfSe analysis identified 22 species to be differentially abundant between the SU and SNU. However, only 7 species maintained a false discovery rate of ≤ 0.2 and could cluster the two groups separately: Rothia mucilaginosa , Streptococcus sp. oral taxon 66, Actinomyces meyeri , Streptococcus vestibularis Streptococcus sanguinis and a potentially novel Veillonella species in association with SU, and Oribacterium asaccharolyticum with SNU. Conclusion Shammah use induces tongue microbiome changes that may be relevant to oral carcinogenesis, namely enrichment of species with high acetaldehyde production potential, which warrants further investigation.

scholarly journals Investigation of Oral Microbiome in Donkeys and the Effect of Dental Care on Oral Microbial Composition

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2245
Author(s):  
Yiping Zhu ◽  
Wuyan Jiang ◽  
Reed Holyoak ◽  
Bo Liu ◽  
Jing Li
Keyword(s):  
Dental Treatment ◽  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Dental Procedures ◽  
Significant Difference ◽  
Dental Diseases ◽  
Rrna Gene Sequencing ◽  
The Impact

The objective of this study was to investigate the oral microbial composition of the donkey and whether basic dental treatment, such as dental floating, would make a difference to the oral microbial environment in donkeys with dental diseases using high-throughput bacterial 16S rRNA gene sequencing. Oral swab samples were collected from 14 donkeys with various dental abnormalities on day 0 (before treatment) and day 20 (twenty days after treatment). It is the first report focusing on the oral microbiome in donkeys with dental diseases and the impact of common dental procedures thereon. Identified in group Day 0 and group Day 20, respectively, were 60,439.6 and 58,579.1 operational taxonomic units (OTUs). Several taxa in Day 0 differed significantly from Day 20 at the phylum and genus levels, but no statistically significant difference was observed in richness and diversity of Day 0 and Day 20. The results also indicated that a larger-scale study focusing on healthy donkey oral microbiome, as well as the correlation of dental diseases and oral microbiomes at different time frames following more specific and consistent dental treatment, are warranted.

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 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 Tongue microbiome of smokeless tobacco users

2020 ◽  
Author(s):  
Esam Halboub ◽  
Mohammed Alakhali ◽  
Abdulwahhab H. Al-Amir ◽  
Husham E. Homeida ◽  
Divyashri Baraniya ◽  
...  
Keyword(s):  
Smokeless Tobacco ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Cross Sectional Study ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Oral Carcinogenesis ◽  
Rothia Mucilaginosa ◽  
Rrna Gene Sequencing

Abstract Background: The possibility that smokeless tobacco may contribute to oral carcinogenesis by influencing the oral microbiome has not been explored. This cross sectional study sought to assess the effect of using hammah, a form of smokeless tobacco prevalent in Arabia, on the tongue microbiome. Tongue scarping samples were obtained from twenty-nine shammah users (SU; 27.34±6.9 years) and 23 shammah non-users (SNU; 27.7±7.19 years) and analyzed with 16S rRNA gene sequencing (V1-V3). Species-level taxonomy assignment of the high-quality, merged reads was obtained using a previously described BLASTn-based algorithm. Downstream analyses were performed with QIIME, LEfSe, and R.Results: A total of 178 species, belonging to 62 genera and 8 phyla were identified. Genera Streptococcus , Leptotrichia , Actinomyces , Veillonella , Haemophilus , Prevotella and Neisseria accounted for more than 60% of the average microbiome. There were no differences between the two groups in species richness and alpha-diversity, but PCoA showed significant separation (P=0.015, ANOSIM). LEfSe analysis identified 22 species to be differentially abundant between the SU and SNU. However, only 7 species maintained a false discovery rate of ≤ 0.2 and could cluster the two groups separately: Rothia mucilaginosa , Streptococcus sp. oral taxon 66, Actinomyces meyeri , Streptococcus vestibularis Streptococcus sanguinis and a potentially novel Veillonella species in association with SU, and Oribacterium asaccharolyticum with SNU.Conclusion: Shammah use induces tongue microbiome changes that may be relevant to oral carcinogenesis, namely enrichment of species with high acetaldehyde production potential, which warrants further investigation.

scholarly journals Identifying prognostic pairwise relationships among bacterial species in microbiome studies

2021 ◽  
Vol 17 (11) ◽  
pp. e1009501
Author(s):  
Sean M. Devlin ◽  
Axel Martin ◽  
Irina Ostrovnaya
Keyword(s):  
Bacterial Species ◽  
Human Microbiome ◽  
16S Rrna Gene Sequencing ◽  
R Package ◽  
Major Influence ◽  
Rrna Gene ◽  
Data Set ◽  
Cancer Data ◽  
Selection Framework ◽  
Rrna Gene Sequencing

In recent literature, the human microbiome has been shown to have a major influence on human health. To investigate this impact, scientists study the composition and abundance of bacterial species, commonly using 16S rRNA gene sequencing, among patients with and without a disease or condition. Methods for such investigations to date have focused on the association between individual bacterium and an outcome, and higher-order pairwise relationships or interactions among bacteria are often avoided due to the substantial increase in dimension and the potential for spurious correlations. However, overlooking such relationships ignores the environment of the microbiome, where there is dynamic cooperation and competition among bacteria. We present a method for identifying and ranking pairs of bacteria that have a differential dichotomized relationship across outcomes. Our approach, implemented in an R package PairSeek, uses the stability selection framework with data-driven dichotomized forms of the pairwise relationships. We illustrate the properties of the proposed method using a published oral cancer data set and a simulation study.

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.

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