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Avila-Arias H, Scharf ME, Turco RF, Richmond DS. Soil Environments Influence Gut Prokaryotic Communities in the Larvae of the Invasive Japanese Beetle Popillia japonica Newman. Front Microbiol 2022; 13:854513. [PMID: 35572692 PMCID: PMC9094118 DOI: 10.3389/fmicb.2022.854513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Invasive scarab beetles, like the Japanese beetle Popillia japonica Newman (JB), spend most of their lives as larvae feeding in the soil matrix. Despite the potential importance of the larval gut microbial community in driving the behavior, physiology, and nutritional ecology of this invasive insect, the role of soil biological and physicochemical characteristics in shaping this community are relatively unknown. Our objectives were to (1) characterize the degree to which larval gut microbial communities are environmentally acquired, (2) examine the combined effects of the gut region (i.e., midgut, hindgut) and local soil environments on gut microbial communities, and (3) search for soil physicochemical correlates that could be useful in future studies aimed at characterizing gut microbial community variation in soil-dwelling scarabs. Gut communities from neonates that were never in contact with the soil were different from gut communities of third instar larvae collected from the field, with neonate gut communities being significantly less rich and diverse. The influence of compartment (soil, midgut, or hindgut) on prokaryotic α- and β-diversity varied with location, suggesting that JB larval gut communities are at least partially shaped by the local environment even though the influence of compartment was more pronounced. Midgut microbiota contained transient communities that varied with the surrounding soil environment whereas hindgut microbiota was more conserved. Prokaryotic communities in the hindgut clustered separately from those of soil and midgut, which displayed greater interspersion in ordination space. Soil cation exchange capacity, organic matter, water holding capacity, and texture were moderately correlated (≥29%) with gut prokaryotic microbial composition, especially within the midgut. Findings suggest that microbial communities associated with the JB gut are partially a function of adaptation to local soil environments. However, conditions within each gut compartment appear to shape those communities in transit through the alimentary canal.
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Affiliation(s)
- Helena Avila-Arias
- Soil Insect Ecology Laboratory, Department of Entomology, Purdue University, West Lafayette, IN, United States
| | - Michael E Scharf
- Entomology and Nematology Department, University of Florida, Gainesville, FL, United States
| | - Ronald F Turco
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Douglas S Richmond
- Soil Insect Ecology Laboratory, Department of Entomology, Purdue University, West Lafayette, IN, United States
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Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton-Marcell J, Gilbert JA, Eisen JA. Bacterial communities associated with cell phones and shoes. PeerJ 2020; 8:e9235. [PMID: 32551196 PMCID: PMC7292020 DOI: 10.7717/peerj.9235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/05/2020] [Indexed: 12/22/2022] Open
Abstract
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.
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Affiliation(s)
- David A Coil
- Genome Center, University of California, Davis, CA, United States of America
| | - Russell Y Neches
- Genome Center, University of California, Davis, CA, United States of America
| | - Jenna M Lang
- Genome Center, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California, Davis, CA, United States of America
| | - Wendy E Brown
- Department of Biomedical Engineering, University of California, Irvine, CA, United States of America.,Science Cheerleaders, Inc., Philadelphia, PA, United States of America
| | - Darlene Cavalier
- Science Cheerleaders, Inc., Philadelphia, PA, United States of America.,SciStarter.org, Philadelphia, PA, United States of America
| | - Jarrad Hampton-Marcell
- Argonne National Laboratory, University of Chicago, Lemont, IL, United States of America
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, UC San Diego School of Medicine, San Diego, CA, United States of America
| | - Jonathan A Eisen
- Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States of America
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Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW, Walker RI, Sack DA, Stine OC. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics 2016; 17:440. [PMID: 27277524 PMCID: PMC4898365 DOI: 10.1186/s12864-016-2777-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/25/2016] [Indexed: 01/01/2023] Open
Abstract
Background Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in inhabitants from low-income countries and in visitors to these countries. The impact of the human intestinal microbiota on the initiation and progression of ETEC diarrhea is not yet well understood. Results We used 16S rRNA (ribosomal RNA) gene sequencing to study changes in the fecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin. Five subjects developed severe diarrhea and seven experienced few or no symptoms. Diarrheal symptoms were associated with high concentrations of fecal E. coli as measured by quantitative culture, quantitative PCR, and normalized number of 16S rRNA gene sequences. Large changes in other members of the microbiota varied greatly from individual to individual, whether or not diarrhea occurred. Nonetheless the variation within an individual was small compared to variation between individuals. Ciprofloxacin treatment reorganized microbiota populations; however, the original structure was largely restored at one and three month follow-up visits. Conclusion Symptomatic ETEC infections, but not asymptomatic infections, were associated with high fecal concentrations of E. coli. Both infection and ciprofloxacin treatment caused variable changes in other bacteria that generally reverted to baseline levels after three months. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2777-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.,Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Joseph N Paulson
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.,Graduate Program in Applied Mathematics & Scientific Computation, University of Maryland, College Park, MD, USA.,Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA.,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | - Irina Astrovskaya
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Brianna R Lindsay
- School of Medicine, University of Maryland, Baltimore, MD, USA.,Merck & Co. Inc, North Wales, PA, USA
| | - Shan Li
- School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Héctor Corrada Bravo
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.,Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Clayton Harro
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Alan W Walker
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.,Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - David A Sack
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - O Colin Stine
- School of Medicine, University of Maryland, Baltimore, MD, USA.
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