Cotton and Surgical Face Masks in Community Settings: Bacterial Contamination and Face Mask Hygiene

During the current COVID-19 pandemic, the use of face masks has become increasingly recommended and even mandatory in community settings. To evaluate the risk of bacterial cross-contamination, this study analyzed the bacterial bioburden of disposable surgical masks and homemade cotton masks, and surveyed the habits and face mask preferences of the Flemish population. Using culture approaches and 16S rRNA gene amplicon sequencing, we analyzed the microbial community on surgical and/or cotton face masks of 13 healthy volunteers after 4 h of wearing. Cotton and surgical masks contained on average 1.46 × 105 CFU/mask and 1.32 × 104 CFU/mask, respectively. Bacillus, Staphylococcus, and Acinetobacter spp. were mostly cultured from the masks and 43% of these isolates were resistant to ampicillin or erythromycin. Microbial profiling demonstrated a consistent difference between mask types. Cotton masks mainly contained Roseomonas, Paracoccus, and Enhydrobacter taxa and surgical masks Streptococcus and Staphylococcus. After 4 h of mask wearing, the microbiome of the anterior nares and the cheek showed a trend toward an altered beta-diversity. According to dedicated questions in the large-scale Corona survey of the University of Antwerp with almost 25,000 participants, only 21% of responders reported to clean their cotton face mask daily. Laboratory results indicated that the best mask cleaning methods were boiling at 100°C, washing at 60°C with detergent or ironing with a steam iron. Taken together, this study suggests that a considerable number of bacteria, including pathobionts and antibiotic resistant bacteria, accumulate on surgical and even more on cotton face masks after use. Based on our results, face masks should be properly disposed of or sterilized after intensive use. Clear guidelines for the general population are crucial to reduce the bacteria-related biosafety risk of face masks, and measures such as physical distancing and increased ventilation should not be neglected when promoting face mask use.

Download Full-text

Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽

10.1186/s12864-020-07307-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gongchao Jing ◽

Yufeng Zhang ◽

Wenzhi Cui ◽

Lu Liu ◽

Jian Xu ◽

...

Keyword(s):

16S Rrna ◽

Large Scale ◽

Low Cost ◽

Human Microbiome ◽

Amplicon Sequencing ◽

Training Sample ◽

Rrna Gene ◽

16S Amplicon Sequencing ◽

Cross Platform ◽

Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

Download Full-text

Undaria pinnatifida exudates trigger shifts in seawater chemistry and microbial communities from Atlantic Patagonian coasts

10.1101/2020.10.21.349233 ◽

2020 ◽

Author(s):

Mariana Lozada ◽

María C. Diéguez ◽

Patricia E. García ◽

Gregorio Bigatti ◽

Juan Pablo Livore ◽

...

Keyword(s):

Large Scale ◽

Undaria Pinnatifida ◽

Synergistic Effects ◽

Amplicon Sequencing ◽

Microbial Populations ◽

Rrna Gene ◽

Seawater Chemistry ◽

Parallel Factor ◽

Complex Organic ◽

Algal Exudates

AbstractThe invasive kelp Undaria pinnatifida has spread from northeastern Asia to temperate coastal environments worldwide, with profound effects on colonized ecosystems. In this work, we analyzed the effect of exudates from U. pinnatifida on the chemical and microbial properties of seawater from a semi-enclosed gulf from Atlantic Patagonia. Exudates of U. pinnatifida, consisting mainly of carbohydrates, were released at a rate of 1.6 ± 0.8 mg C g−1 algae day−1, affecting the quality and optical properties of seawater in experimental incubations. Parallel factor analysis based on excitation-emission matrices collected from exudates revealed the presence of two humic-like and one non-humic fluorescent components. Exudate release stimulated microbial growth and polysaccharide degrading activity in seawater. After a 7-day incubation of fresh seawater with the exudates, changes in microbial community structure were analyzed by large-scale 16S rRNA gene amplicon sequencing. Copiotrophic and fermentative genera such as Spirochaeta (Spirochaetes) and Propionigenium (Fusobacteria) increased in the incubations with algal exudates. Genomic potential prediction revealed that the selected bacterial community could have higher ribosome content - an indicator of the potential for reaching higher metabolic rates - and genes for the degradation of complex organic compounds such as polysaccharides and other carbohydrates present in the exudates. Nutrient addition triggered the emergence of other microbial populations with different ecophysiological niches: unclassified Flavobacteriales, unclassified bacteria related to the recently described Phylum Kiritimatiellaeota, as well as potential pathogens such as Vibrio (Gammaproteobacteria) and Arcobacter (Epsilonproteobacteria), suggesting potential synergistic effects between invasive macroalgae and human activities.

Download Full-text

Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes

Frontiers in Microbiology ◽

10.3389/fmicb.2021.678319 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wenyi Xu ◽

Tianda Chen ◽

Yuwei Pei ◽

Hao Guo ◽

Zhuanyu Li ◽

...

Keyword(s):

Large Scale ◽

Low Cost ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Shotgun Sequencing ◽

Taxonomic Resolution ◽

Rrna Gene ◽

Cost Efficient ◽

Taxonomic Assignments

Characterization of the bacterial composition and functional repertoires of microbiome samples is the most common application of metagenomics. Although deep whole-metagenome shotgun sequencing (WMS) provides high taxonomic resolution, it is generally cost-prohibitive for large longitudinal investigations. Until now, 16S rRNA gene amplicon sequencing (16S) has been the most widely used approach and usually cooperates with WMS to achieve cost-efficiency. However, the accuracy of 16S results and its consistency with WMS data have not been fully elaborated, especially by complicated microbiomes with defined compositional information. Here, we constructed two complex artificial microbiomes, which comprised more than 60 human gut bacterial species with even or varied abundance. Utilizing real fecal samples and mock communities, we provided solid evidence demonstrating that 16S results were of poor consistency with WMS data, and its accuracy was not satisfactory. In contrast, shallow whole-metagenome shotgun sequencing (shallow WMS, S-WMS) with a sequencing depth of 1 Gb provided outputs that highly resembled WMS data at both genus and species levels and presented much higher accuracy taxonomic assignments and functional predictions than 16S, thereby representing a better and cost-efficient alternative to 16S for large-scale microbiome studies.

Download Full-text

Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles

PeerJ ◽

10.7717/peerj.6172 ◽

2019 ◽

Vol 7 ◽

pp. e6172 ◽

Cited By ~ 8

Author(s):

Yun Kit Yeoh ◽

Zigui Chen ◽

Mamie Hui ◽

Martin C.S. Wong ◽

Wendy C.S. Ho ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Individual Variation ◽

Large Scale ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Relative Effect ◽

Individual Variability ◽

Rrna Gene ◽

Sample Collection

Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.

Download Full-text

Identification and differentiation of Pseudomonas species in field samples using an rpoD amplicon sequencing methodology

10.1101/2021.06.08.447643 ◽

2021 ◽

Author(s):

Jonas Greve Lauritsen ◽

Morten Lindqvist Hansen ◽

Pernille Kjersgaard Bech ◽

Lars Jelsbak ◽

Lone Gram ◽

...

Keyword(s):

16S Rrna ◽

Large Scale ◽

Sampling Site ◽

Amplicon Sequencing ◽

Soil Samples ◽

Species Differentiation ◽

Rrna Gene ◽

Rpod Gene ◽

Field Samples ◽

Pseudomonas Species

Species of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural or industrial settings, the organisms must be profiled at species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760 nt region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a sixteen membered Pseudomonas species mock community. All 16 species were correctly and semi-quantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3V4 amplicon sequencing only correctly identified one species. We analysed the Pseudomonas profile in thirteen soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the microbial community, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and ten from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD-amplicon approach identified more species than found by cultivation, including hard-to-culture non-fluorescent pseudomonads, as well as more than found by 16S rRNA V3V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method.

Download Full-text

Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period

Frontiers in Microbiology ◽

10.3389/fmicb.2021.700637 ◽

2021 ◽

Vol 12 ◽

Author(s):

Suhyun Kim ◽

Md. Rashedul Islam ◽

Ilnam Kang ◽

Jang-Cheon Cho

Keyword(s):

16S Rrna ◽

High Throughput ◽

Large Scale ◽

Phylogenetic Analyses ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Taxonomic Groups ◽

Bacterial Groups

Although many culture-independent molecular analyses have elucidated a great diversity of freshwater bacterioplankton, the ecophysiological characteristics of several abundant freshwater bacterial groups are largely unknown due to the scarcity of cultured representatives. Therefore, a high-throughput dilution-to-extinction culturing (HTC) approach was implemented herein to enable the culture of these bacterioplankton lineages using water samples collected at various seasons and depths from Lake Soyang, an oligotrophic reservoir located in South Korea. Some predominant freshwater bacteria have been isolated from Lake Soyang via HTC (e.g., the acI lineage); however, large-scale HTC studies encompassing different seasons and water depths have not been documented yet. In this HTC approach, bacterial growth was detected in 14% of 5,376 inoculated wells. Further, phylogenetic analyses of 16S rRNA genes from a total of 605 putatively axenic bacterial cultures indicated that the HTC isolates were largely composed of Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. Importantly, the isolates were distributed across diverse taxa including phylogenetic lineages that are widely known cosmopolitan and representative freshwater bacterial groups such as the acI, acIV, LD28, FukuN57, MNG9, and TRA3–20 lineages. However, some abundant bacterial groups including the LD12 lineage, Chloroflexi, and Acidobacteria could not be domesticated. Among the 71 taxonomic groups in the HTC isolates, representative strains of 47 groups could either form colonies on agar plates or be revived from frozen glycerol stocks. Additionally, season and water depth significantly affected bacterial community structure, as demonstrated by 16S rRNA gene amplicon sequencing analyses. Therefore, our study successfully implemented a dilution-to-extinction cultivation strategy to cultivate previously uncultured or underrepresented freshwater bacterial groups, thus expanding the basis for future multi-omic studies.

Download Full-text

Impact of time and temperature on gut microbiota and SCFA composition in stool samples

10.1101/2020.04.01.20049841 ◽

2020 ◽

Cited By ~ 1

Author(s):

Janet L. Cunningham ◽

Ludvig Bramstång ◽

Abhijeet Singh ◽

Shishanthi Jayarathna ◽

Annica J. Rasmusson ◽

...

Keyword(s):

Gut Microbiota ◽

Large Scale ◽

Lactobacillus Reuteri ◽

Amplicon Sequencing ◽

Storage Conditions ◽

Resonance Spectroscopy ◽

Rrna Gene ◽

Microbial Composition ◽

Laboratory Errors ◽

Stool Samples

AbstractGut dysbiosis has been implicated in the pathophysiology of a growing number of non-communicable diseases. High through-put sequencing technologies and short chain fatty acid (SCFA) profiling enables surveying of the composition and function of the gut microbiota and provide key insights into host-microbiome interactions. However, a methodological problem with analyzing stool samples is that samples are treated and stored differently prior to submission for analysis potentially influencing the composition of the microbiota and its metabolites. In the present study, we simulated the sample acquisition of a large-scale study, in which stool samples were stored for up to two days in the fridge or at room temperature before being handed over to the hospital. To assess the influence of time and temperature on the microbial community and on SCFA composition in a controlled experimental setting, the stool samples of 10 individuals were exposed to room and fridge temperatures for 24 and 48 hours, respectively, and analyzed using 16S rRNA gene amplicon sequencing, qPCR and nuclear magnetic resonance spectroscopy. To best of our knowledge, this is the first study to investigate the influence of storage time and temperature on the absolute abundance of methanogens, and of Lactobacillus reuteri. The results indicate that values obtained for methanogens, L. reuteri and total bacteria are still representative even after storage for up to 48 hours at RT (20°C) or 4°C. The overall microbial composition and structure appeared to be influenced more by laboratory errors introduced during sample processing than by the actual effects of temperature and time. Although microbial activity was demonstrated by elevated SCFA at both 4 °C and RT, SCFAs ratios were more stable over the different conditions and may be considered as long as samples are come from similar storage conditions.

Download Full-text

Transient and Persistent Gastric Microbiome: Adherence of Bacteria in Gastric Cancer and Dyspeptic Patient Biopsies after Washing

Journal of Clinical Medicine ◽

10.3390/jcm9061882 ◽

2020 ◽

Vol 9 (6) ◽

pp. 1882 ◽

Cited By ~ 1

Author(s):

Malene R. Spiegelhauer ◽

Juozas Kupcinskas ◽

Thor B. Johannesen ◽

Mindaugas Urba ◽

Jurgita Skieceviciene ◽

...

Keyword(s):

Gastric Cancer ◽

Bacterial Diversity ◽

Large Scale ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Peptic Ulcers ◽

Gastric Biopsies ◽

H Pylori ◽

Gastric Microbiota

Helicobacter pylori is a common colonizer of the human stomach, and long-term colonization has been related to development of atrophic gastritis, peptic ulcers and gastric cancer. The increased gastric pH caused by H. pylori colonization, treatment with antibiotics or proton pump inhibitors (PPI) may allow growth of other bacteria. Previous studies have detected non-Helicobacter bacteria in stomach biopsies, but no conclusion has been made of whether these represent a transient contamination or a persistent microbiota. The aim of this study was to evaluate the transient and persistent bacterial communities of gastric biopsies. The washed or unwashed gastric biopsies were investigated by cultivation and microbiota analysis (16S rRNA gene-targeted amplicon sequencing) for the distribution of H. pylori and other non-Helicobacter bacteria. The number of cultured non-Helicobacter bacteria decreased in the washed biopsies, suggesting that they might be a transient contamination. No significant differences in the bacterial diversity were observed in the microbiome analysis between unwashed and washed biopsies. However, the bacterial diversity in biopsies shown H. pylori-positive and H. pylori-negative were significantly different, implying that H. pylori is the major modulator of the gastric microbiome. Further large-scale studies are required to investigate the transient and persistent gastric microbiota.

Download Full-text

Phyto-fabrication of Iron Nanoparticles: Characterization and Antibacterial Capacity

Current Nanoscience ◽

10.2174/1573413716999200817105934 ◽

2020 ◽

Vol 16 ◽

Author(s):

Asma S. Algebaly ◽

Afrah E. Mohammed ◽

Mudawi M. Elobeid

Keyword(s):

Electron Microscopy ◽

Plant Extracts ◽

Large Scale ◽

Iron Nanoparticles ◽

Ethanolic Extract ◽

Green Technology ◽

Resistant Bacteria ◽

Scale Production ◽

Bacterial Strains ◽

Plant Sources

Introduction: Fabrication of iron nanoparticles (FeNPs) has recently gained a great concern for their varied applications in remediation technologies of the environment. Objective: The current study aimed to fabricate iron nanoparticles by green technology approach using different plant sources, Azadirachta indica leaf and Calligonum comosum root following two extraction methods. Methods: Currently, a mixture of FeCl2 and FeCl3 was used to react with the plant extracts which are considered as reducing and stabilizing agents for the generation of FeNPs in one step. Different techniques were used for FeNPs identification. Results: Immediately after mixing of the two reaction components, the color changed to dark brown as an indication of safe conversion of Fe ions to FeNPs, that later confirmed by zeta sizer, transmission electron microscopy (TEM) and scanning electron microscopy (SEM). FeNPs fabricated by C. comosum showed smaller size when compared by those fabricated by A. indica. Using both plant sources, FeNPs fabricated by the aqueous extract had smaller size in relation to those fabricated by ethanolic extract. Furthermore, antibacterial ability against two bacterial strains was approved. Conclusion: The current results indicated that, at room temperature plant extracts fabricated Fe ion to Fe nanoparticles, suggesting its probable usage for large scale production as well as its suitability against bacteria. It could also be recommended for antibiotic resistant bacteria.

Download Full-text

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

Download Full-text