scholarly journals Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls with cpn 60-Based Microbiome Profiling

2021 ◽  
Author(s):  
Scott J. Dos Santos ◽  
Zahra Pakzad ◽  
Chelsea N. Elwood ◽  
Arianne Y. K. Albert ◽  
Soren Gantt ◽  
...  
Keyword(s):  
Recent Work ◽  
Bacterial Communities ◽  
Microbial Colonization ◽  
Negative Controls ◽  
Microbiome Profiling ◽  
Cpn 60

Much like the recent placental microbiome controversy, studies of neonatal meconium reporting bacterial communities within the fetal and neonatal gut imply that microbial colonization begins prior to birth. However, recent work has shown that placental microbiomes almost exclusively represent contamination from lab reagents and the environment.

scholarly journals 16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients

2017 ◽  
Author(s):  
Sarah K. Lucas ◽  
Robert Yang ◽  
Jordan M. Dunitz ◽  
Holly C. Boyer ◽  
Ryan C. Hunter
Keyword(s):  
Cystic Fibrosis ◽  
Bacterial Communities ◽  
Gene Sequencing ◽  
Microbial Colonization ◽  
Sinus Surgery ◽  
Lower Airway ◽  
Rrna Gene ◽  
Inflammatory Disorder ◽  
Airway Infections ◽  
Lower Airways

ABSTRACTRationaleChronic rhinosinusitis (CRS) is an inflammatory disorder of the sinonasal mucosa associated with microbial colonization. Metastasis of sinus microbiota into the lower airways is thought have significant implications in the development of chronic respiratory disease. However, this dynamic has not been thoroughly investigated in cystic fibrosis (CF) patients, where lower airway infections are the primary driver of patient mortality. Given the high prevalence of CRS in CF patients and the proposed infection dynamic between the upper and lower airways, a better understanding of sinus-lung continuum is warranted.ObjectiveTo compare the microbiome of matched sinus mucus and lung sputum samples from CF subjects undergoing functional endoscopic sinus surgery (FESS) for treatment of CRS.MethodsMucus was isolated from the sinuses and lungs of twelve CF patients undergoing FESS. 16S ribosomal RNA gene sequencing was then performed to compare bacterial communities of the CF lung and sinus niches. Finally, functional profiling was performed to predict bacterial metagenomes from the 16S dataset, and was used to compare pathogenic bacterial phenotypes between the upper and lower airways.Measurements and Main ResultsBacterial richness was comparable between airway sites, though sinus and lung environments differed in community evenness, with the sinuses harboring a higher prevalence of dominant microorganisms. Beta diversity metrics also revealed that samples clustered more consistently by airway niche rather than by individual. Finally, predicted metagenomes showed that anaerobic metabolism was enriched in the lung environment, while genes associated with both biofilm formation and Gram identity were not variable between sites.ConclusionsSinus and lung microbiomes are distinct with respect to richness and evenness, while sinus communities have a higher incidence of a dominant taxon. Additionally, ordination analyses point to sinus and lung environments as being stronger determinants of microbial community structure than the individual patient. Finally, BugBase-predicted metagenomes revealed anaerobic phenotypes to be in higher abundance in the lung relative to the sinuses. Our findings indicate that while the paranasal sinuses and lungs may still comprise a unified airway in which lower airways are seeded by sinus microbiota, these discrete airway microenvironments harbor distinct bacterial communities.

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 Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Edoardo Puglisi ◽  
Francesco Romaniello ◽  
Serena Galletti ◽  
Enrico Boccaleri ◽  
Alberto Frache ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Bacterial Colonization ◽  
Chemical Properties ◽  
Microbial Colonization ◽  
Β Diversity ◽  
Physico Chemical ◽  
Plastic Type ◽  
Plastic Wastes ◽  
Ft Raman Spectroscopy ◽  
Degradation Degree

Abstract The microbial colonization of plastic wastes has been extensively studied in marine environments, while studies on aged terrestrial wastes are scarce, and mostly limited to the isolation of plastic-degrading microorganisms. Here we have applied a multidisciplinary approach involving culturomics, next-generation sequencing analyses and fine-scale physico-chemical measurements to characterize plastic wastes retrieved in landfill abandoned for more than 35 years, and to assess the composition of bacterial communities thriving as biofilms on the films’ surfaces. All samples were characterized by different colors but were all of polyethylene; IR and DSC analyses identified different level of degradation, while FT-Raman spectroscopy and X-ray fluorescence further assessed the degradation level and the presence of pigments. Each plastic type harbored distinct bacterial communities from the others, in agreement with the differences highlighted by the physico-chemical analyses. Furthermore, the most degraded polyethylene films were found to host a bacterial community more similar to the surrounding soil as revealed by both α- and β-diversity NGS analyses. This work confirms the novel hypothesis that different polyethylene terrestrial waste samples select for different bacterial communities, and that structure of these communities can be correlated with physico-chemical properties of the plastics, including the degradation degree.

scholarly journals Textile waste and microplastic induce activity and development of unique hydrocarbon-degrading marine bacterial communities

2020 ◽  
Author(s):  
Elsa B. Girard ◽  
Melanie Kaliwoda ◽  
Wolfgang W. Schmahl ◽  
Gert Wörheide ◽  
William D. Orsi
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Metabolic Response ◽  
Microbial Colonization ◽  
Sequencing Data ◽  
Hydrocarbonoclastic Bacteria ◽  
Textile Fibers ◽  
Textile Waste ◽  
Marine Habitats ◽  
Metabolic Stimulation

ABSTRACTBiofilm-forming microbial communities on plastics and textile fibers are of growing interest since they have potential to contribute to disease outbreaks and material biodegradability in the environment. Knowledge on microbial colonization of pollutants in the marine realm is expanding, but metabolic responses during substrate colonization remains poorly understood. Here, we assess the metabolic response in marine microbial communities to three different micropollutants, virgin high-density polyethylene (HDPE) microbeads, polysorbate-20 (Tween), and textile fibers. Intertidal textile fibers, mainly cotton, virgin HDPE, and Tween induced variable levels of microbial growth, respiration, and community assembly in controlled microcosm experiments. RAMAN characterization of the chemical composition of the textile waste fibers and high-throughput DNA sequencing data shows how the increased metabolic stimulation and biodegradation is translated into selection processes ultimately manifested in different communities colonizing the different micropollutant substrates. The composition of the bacterial communities colonizing the substrates were significantly altered by micropollutant substrate type and light conditions. Bacterial taxa, closely related to the well-known hydrocarbonoclastic bacteria Kordiimonas spp. and Alcanivorax spp., were enriched in the presence of textile-waste. The findings demonstrate an increased metabolic response by marine hydrocarbon-degrading bacterial taxa in the presence of microplastics and textile waste, highlighting their biodegradation potential. The metabolic stimulation by the micropollutants was increased in the presence of light, possibly due to photochemical dissolution of the plastic into smaller bioavailable compounds. Our results suggest that the development and increased activity of these unique microbial communities likely play a role in the bioremediation of the relatively long lived textile and microplastic pollutants in marine habitats.Graphical Abstract

scholarly journals Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8058 ◽  
Author(s):  
Rittik Deb ◽  
Ashwin Nair ◽  
Deepa Agashe
Keyword(s):  
Gut Microbiota ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Microbial Colonization ◽  
Generalist Predators ◽  
Sampling Location ◽  
Strongly Correlated ◽  
Dietary Specialization ◽  
Host Identity ◽  
Abundance And Distribution

Host-associated gut microbiota can have significant impacts on host ecology and evolution and are often host-specific. Multiple factors can contribute to such host-specificity: (1) host dietary specialization passively determining microbial colonization, (2) hosts selecting for specific diet-acquired microbiota, or (3) a combination of both. The latter possibilities indicate a functional association and should produce stable microbiota. We tested these alternatives by analyzing the gut bacterial communities of six species of wild adult dragonfly populations collected across several geographic locations. The bacterial community composition was predominantly explained by sampling location, and only secondarily by host identity. To distinguish the role of host dietary specialization and host-imposed selection, we identified prey in the guts of three dragonfly species. Surprisingly, the dragonflies–considered to be generalist predators–consumed distinct prey; and the prey diversity was strongly correlated with the gut bacterial profile. Such host dietary specialization and spatial variation in bacterial communities suggested passive rather than selective underlying processes. Indeed, the abundance and distribution of 72% of bacterial taxa were consistent with neutral community assembly; and fluorescent in situ hybridization revealed that bacteria only rarely colonized the gut lining. Our results contradict the expectation that host-imposed selection shapes the gut microbiota of most insects, and highlight the importance of joint analyses of diet and gut microbiota of natural host populations.

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