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Metagenomic Shotgun Sequencing Provides Prevalence Data for Pathogens, and Source-Tracking Indices Useful in Public Health Risk Assessment of Environmental Waters

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Journal of Geoscience and Environment Protection 2020年第6期8卷 115-129页

作者： Brian Mercer karim dawkins Lisa Meday Nwadiuto Esiobu Microbial Biotech Lab Sanson Building Florida Atlantic University Boca Raton USA Environmental Resource Management Department Water Quality Seminole Tribe of Florida Holywood USA

State-approved membrane filtration (MF) techniques for water quality assessments were contrasted with metagenomic shotgun sequencing (MSS) protocols to evaluate their efficacy in providing precise health-risk indices for surface waters. Samples from a freshwater receiving pond (ABI-1002) and two upstream storm water ditches (ABI-1003) and (ABI-1004) yielded alarmingly high Fecal coliform MF densities of 220, >2000 and >2000 CFU/100ml respectively. The indicator, Enterococcus bacteria exceeded allowable limits in all but the equipment control (ABI-1001). Using MSS, the relative numerical abundance of pathogenic bacteria, virulence and antibiotic resistance genes revealed the status and potential pollution sources of each ditch. High levels of Shigella sp. (0 (ABI-1001), 4945 (ABI-1002), 55,008 (ABI-1003), and 2221 (ABI-1004) genomic reads/100ml) correlated with virulence genes and antibiotic resistance genes found in fecal samples for ABI1003 and not ABI1004. Traditional culture methods (TCM) showed possible fecal contamination in two of the four samples, and no contamination in the others. MSS clearly distinguished between fecal and environmental bacteria contamination sources, and pinpointed actual risks from pathogens. Our data underscore the potential utility of MSS in precision risk assessment for public and biodiversity health and tracking of environmental microbiomes shifts by field managers and policy makers.

关键词： Metagenomic Shotgun Sequencing Water Quality Risk Assessment Indicator Bacteria Environmental Microbiomes

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Prevalence and Disinfection of Bacteria Associated with Various Types of Wristbands

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Advances in Infectious Diseases 2023年第2期13卷 193-209页

作者： Joseph Mendonca Belen Wertheimer Daynalee Dixon Bodhi Stone karim dawkins Miranda Christian Nwadiuto Esiobu Microbial Biotechnology Laboratory Department of Biological Sciences Florida Atlantic University Boca Raton FL USA West Palm Beach TV (WPTV) West Palm Beach FL USA

The potential role of personal items in the transmission of pathogens is poorly understood. In this study, we cultured bacteria of public health importance found on wristbands, determined whether there is a correlation between wristband material and prevalence, and tested three household disinfectants for efficacy in reducing bacteria on wristbands made of plastic, rubber, metal, and cloth, using standard microbiological assays. Total cultivable bacteria, Staphylococci, Enterobacteria (Escherichia coli), and Pseudomonas on 20 smartwatch wristbands were cultured from randomly recruited subjects. Nearly all wristbands (95%) were contaminated, with the highest average numbers of 3.46E+4 cfu/cm2 and 1.52E+4 cfu/cm2 on rubber and plastic bands respectively. Metallic gold and silver wristbands had zero to 18 cfu/cm2. While the high prevalence of Staphylococcus spp (85% of wristbands)—skin microbiota;was not unexpected, the occurrence of Pseudomonas spp (30%), and enteric bacteria (60%), even at relatively low numbers is of public health significance. Bacterial load on individual subjects varied remarkably with males and females harboring average total bacteria of 4.045 and 3.42 log10cfu/cm2 of wristband, respectively. The most important predictor of wristband bacteria load was the texture of wristband material and activity (hygiene) of the subject at sampling time. Potential pathogens—Staphylococcus aureus (8143 cfu/cm2) and Pseudomonas spp. (1126 cfu/cm2) were most abundant on cloth and rubber wristbands, respectively, while the presence of the E. coli group was associated with animal handling activity by a veterinarian. Lysol Disinfectant Spray and 70% Ethanol were highly effective regardless of wristband material with >99.99% kill rate and a log cfu/cm2 reduction of 3 - 4.0 and 3 - 4.5 respectively within 30 seconds. Apple Cider Vinegar (ACV) was not as potent. Only 2 - 3.5 log cfu/

关键词： Apple Cider Vinegar Disinfectants Escherichia coli Lysol Pseudomonas aeruginosa Public Health Staphylococcus aureus Wristbands

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Analysis of a Tropical Warm Spring Microbiota Using 16S rRNA Metabarcoding

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Advances in Microbiology 2020年第4期10卷 145-165页

作者： Deborah Fasesan karim dawkins Roberto Ramirez Hadiza Rasheed-Jada Abiodun Onilude Oyekanmi Nash Nwadiuto Esiobu Center for Genomics Research and Innovation National Biotechnology Development Agency Abuja Nigeria Department of Microbiology University of Ibadan Ibadan Nigeria Microbial Biotechnology Laboratory Florida Atlantic University Boca Raton USA

The Ikogosi Warm Spring is a unique ecological niche in Western Nigeria with an average temperature and pH of 38°C and 5.8 respectively. It mixes with an adjacent cold spring (28°C & pH 7.6), about 100 meters from source, yielding a confluence body of water of 32°C and pH 7.7. To explore the bacterial community structure of this uncommon environment and to scan for potentially useful bacteria, metagenomes extracted directly from five samples (source and mid-point of warm spring;source and midpoint of cold spring, and the confluence) were analyzed. Using the MiSeq Illumina next generation sequencing protocols, the V3-V4 region of the 16S rRNA gene pool was sequenced and analyzed by QIIME (Quantitative Insights into Microbial Ecology) and R software. At least 11% (47,446) of all the sequences were unknown to any of the databases employed. Bacterial diversity and abundance at the source of both springs were extremely low, accounting for less than 0.07% of the total sequence reads at the confluence, 100 m downstream. In contrast to the highly diversified mesophilic confluence community where 21 different phyla were identified, only 4 and 5 phyla were recovered from the source-point of the warm spring and cold spring respectively. The most prevalent phyla in all samples were members of the versatile Proteobacteria (35% - 50% relative abundance), and the hardy Firmicutes (33% - 40%). Operational taxonomic units (OTUs) obtained from all the samples averaged at 1414. Temperature and pH were equally significant predictors of genomic diversity and richness, with the warm and cold spring sources having less than 5 bacteria phyla. Exiguobacterium sp. (a potential plastic degrader) and other deep rooted bacteria were found in the warm spring while the cold spring outflow contained among others such as Rubrobacter sp. and Chloroflexi sp. (which is close to the phylogenetic root of the domain Bacteria). Many taxonomically unresolved sequences could indicate the presence of potenti

关键词： Ikogosi Warm Springs Amplicon Metagenomics Next-Gen Sequencing QIIME Bacterial Diversity Source

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Microbiomes of Top and Sub-Layers of Semi-Arid Soils in North-Eastern Nigeria Are Rich in Firmicutes and Proteobacteria with Surprisingly High Diversity of Rare Species

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Advances in Microbiology 2019年第1期9卷 102-118页

作者： Mwajim Bukar Oluwole Sodipo karim dawkins Roberto Ramirez Jummai T. Kaldapa Martha Tarfa Nwadiuto Esiobu North-East Zonal Biotechnology Centre of Excellence University of Maiduguri Maiduguri Nigeria Biochemistry Department Faculty of Science University of Maiduguri Maiduguri Nigeria Biological Sciences Department Microbial Biotech Laboratory Florida Atlantic University Boca Raton FL USA

Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility,

关键词： Microbiomes Semi-Arid Soils Microbial Community Structure Soil Bacteria Soil Fertility Top-Soil Re-Vegetation Proteobacteria Firmicutes Sub-Surface OTU

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