Absolute Bacterial Abundances Research Articles

The spatial and temporal effect of electrochromic windows on indoor and human microbiome in an inpatient hospital.

Improving the hospital environment and developing novel disinfection strategies are critical for infection control in healthcare settings. In this study, we explored the effects of electrochromic (EC) windows on indoor and patient microbiome in an inpatient hospital. Hematology-Oncology patients at the University of Vermont Medical Center. We conducted a prospective study in ten occupied patient rooms. Five of the patient rooms had active EC windows that tint dynamically to control for heat and glare, and the other five rooms had deactivated EC windows that simulated traditional windows and blinds. Samples were collected one day before patient admission as baseline and on the 1st, 3rd, and 5th day of the patient stay. Total bacterial abundance and bacterial community structure were determined through quantitative PCR and 16s rRNA Illumina MiSeq sequencing, respectively. Patient rooms with active EC windows had significantly lower light intensity and temperature than traditional patient rooms with blinds. The absolute bacterial abundance and diversities on windows were significantly lower in rooms with EC windows and the bacterial composition changed after one day EC window activation. Compared to baseline, relative abundance of the Staphylococcus genus was significantly lower on EC window surface during the five-day experiment. In contrast, the air microbiome was more diverse in rooms with EC windows. Active electrochromic (EC) windows in patient rooms result in lower light intensity and temperature, reduced bacterial abundance and diversities on window surfaces, and a more diverse air microbiome, informing future healthcare design.

Quantitative insights into effects of intrapartum antibiotics and birth mode on infant gut microbiota in relation to well-being during the first year of life

ABSTRACT Birth mode and maternal intrapartum (IP) antibiotics affect infants’ gut microbiota development, but their relative contribution to absolute bacterial abundances and infant health has not been studied. We compared the effects of Cesarean section (CS) delivery and IP antibiotics on infant gut microbiota development and well-being over the first year. We focused on 92 healthy infants born between gestational weeks 37–42 vaginally without antibiotics (N = 26), with IP penicillin (N = 13) or cephalosporin (N = 7) or by CS with IP cephalosporin (N = 33) or other antibiotics (N = 13). Composition and temporal development analysis of the gut microbiota concentrated on 5 time points during the first year of life using 16S rRNA gene amplicon sequencing, integrated with qPCR to obtain absolute abundance estimates. A mediation analysis was carried out to identify taxa linked to gastrointestinal function and discomfort (crying, defecation frequency, and signs of gastrointestinal symptoms), and birth interventions. Based on absolute abundance estimates, the depletion of Bacteroides spp. was found specifically in CS birth, while decreased bifidobacteria and increased Bacilli were common in CS birth and exposure to IP antibiotics in vaginal delivery. The abundances of numerous taxa differed between the birth modes among cephalosporin-exposed infants. Penicillin had a milder impact on the infant gut microbiota than cephalosporin. CS birth and maternal IP antibiotics had both specific and overlapping effects on infants’ gut microbiota development. The resulting deviations in the gut microbiota are associated with increased defecation rate, flatulence, perceived stomach pain, and intensity of crying in infancy.

Modulation of the food microbiome by apple fruit processing

During the early life, introduction to external exposures such as consumption of solid foods contribute to the development of the gut microbiota. Among solid foods, fruit and vegetables are normally consumed during early childhood making them key components of a healthy human diet. The role of the indigenous microbiota of fruits as a source for beneficial gut microbes, especially during food processing, is largely unknown. Therefore, we investigated the apple fruit microbiota before and after processing using functional assays, advanced microscopic as well as sequencing technologies. Apple fruits carried a high absolute bacterial abundance (1.8 × 105 16S rRNA copies per g of apple pulp) and diversity of bacteria (Shannon diversity index = 2.5). We found that heat and mechanical treatment substantially affected the fruit's microbiota following a declining gradient of absolute bacterial abundance and bacterial diversity from shredded > boiled > pureed > preserved > dried apples. Betaproteobacteriales and Enterobacteriales were the two dominant bacterial orders (51.3%, 20.4% of the total 16S rRNA sequence reads) in the unprocessed apple. Boiling and air drying reduced the microbial load, but an unexpected, substantial fraction of 1/3 of the microbiota survived. Boiling and air drying shifted the microbiota leading to a relative increase in low abundant taxa such as Pseudomonas and Ralstonia (>2 log2 fold change), while others such as Bacillus decreased. Bacillus spp., frequently found in raw fruits, were shown to have specific traits, i.e. antagonist activity against opportunistic pathogens, biosurfactant production, and bile salt resistance indicating a probiotic potential. Our findings provide novel insights into food microbial changes during processing and demonstrate that food microbiome studies need a combined methodological approach. Food inhabiting microbes, currently considered being a risk factor for food safety, are a potential resource for the infant gut microbiome.

Response of Prokaryotic Communities to Freshwater Salinization

Each year, millions of tons of sodium chloride are dumped on roads, contributing to the salinization of freshwater environments. Thus, we sought to understand the effect of sodium chloride (NaCl) on freshwater lake prokaryotic communities, an important and understudied component of food webs. Using mesocosms with 0.01–2.74 ppt NaCl (0.27–1110.86 mg/L Cl−), we evaluated the effect generated on the diversity and absolute abundance of prokaryotic populations after three and six weeks. A positive relationship between Cl− values and absolute bacterial abundance was found after three weeks. The influence of eukaryotic diversity variation was observed as well. Significant differentiation of bacterial communities starting at 420 mg/L Cl− was observed after three weeks, levels lower than the Canadian and US recommendations for acute chloride exposure. The partial recovery of a “pre-disturbance” community was observed following a drop in salinity at the threshold level of 420 mg/L Cl−. A gradual transition of dominance from Betaproteobacteria and Actinobacteria to Bacteroidia and Alphaproteobacteria was observed and is overall similar to the natural transition observed in estuaries.

Fate and impact of wastewater-borne micropollutants in lettuce and the root-associated bacteria

The reuse of water for agricultural practices becomes progressively more important due to increasing demands for a transition to a circular economy. Treated wastewater can be an alternative option of blue water used for the irrigation of crops but its risks need to be evaluated. This study assesses the uptake and metabolization of pharmaceuticals and personal care products (PPCPs) derived from treated wastewater into lettuce as well as the impact on root-associated bacteria under a realistic and worst-case scenario. Lettuce was grown in a controlled greenhouse and irrigated with water or treated wastewater spiked with and without a mixture of fourteen different PPCPs at 10 μg/L or 100 μg/L. After harvesting the plants, the same soil was reused for a consecutive cultivation campaign to test for the accumulation of PPCPs. Twelve out of fourteen spiked PPCPs were detected in lettuce roots, and thirteen in leaves. In roots, highest concentrations were measured for sucralose, sulfamethoxazole and citalopram, while sucralose, acesulfame and carbamazepine were the highest in leaves. Higher PPCP concentrations were found in lettuce roots irrigated with spiked treated wastewater than in those irrigated with spiked water. The absolute bacterial abundance remained stable over both cultivation campaigns and was not affected by any of the treatments (type of irrigation water (water vs. wastewater) nor concentration of PPCPs). However, the irrigation of lettuce with treated wastewater had a significant effect on the microbial α-diversity indices at the end of the second cultivation campaign, and modified the structure and community composition of root-associated bacteria at the end of both campaigns. Five and fourteen bacterial families were shown to be responsible for the observed changes at the end of the first and second cultivation campaign, respectively. Relative abundance of Haliangium and the clade Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium was significantly affected in response to PCPPs exposure. Caulobacter, Cellvibrio, Hydrogenophaga and Rhizobacter were significantly affected in microcosms irrigated with wastewater.

Long-term fertilization and tillage regimes have limited effects on structuring bacterial and denitrifier communities in a sandy loam UK soil.

Denitrification causes loss of available nitrogen from soil systems, thereby reducing crop productivity and increasing reliance on agrochemicals. The dynamics of denitrification and denitrifying communities are thought to be altered by land management practices, which affect the physicochemical properties of the soil. In this study, we look at the effects of long-term tillage and fertilization regimes on arable soils following 16 years of treatment in a factorial field trial. By studying the bacterial community composition based on 16S rRNA amplicons, absolute bacterial abundance and diversity of denitrification functional genes (nirK, nirS and nosZ), under conditions of minimum/conventional tillage and organic/synthetic mineral fertilizer, we tested how specific land management histories affect the diversity and distribution of both bacteria and denitrification genes. Bacterial and denitrifier communities were largely unaffected by land management history and clustered predominantly by spatial location, indicating that the variability in bacterial community composition in these arable soils is governed by innate environmental differences and Euclidean distance rather than agricultural management intervention.

Equivolumetric Protocol Generates Library Sizes Proportional to Total Microbial Load in 16S Amplicon Sequencing.

High-throughput sequencing of 16S rRNA amplicon has been extensively employed to perform microbiome characterization worldwide. As a culture-independent methodology, it has allowed high-level profiling of sample bacterial composition directly from samples. However, most studies are limited to information regarding relative bacterial abundances (sample proportions), ignoring scenarios in which sample microbe biomass can vary widely. Here, we use an equivolumetric protocol for 16S rRNA amplicon library preparation capable of generating Illumina sequencing data responsive to input DNA, recovering proportionality between observed read counts and absolute bacterial abundances within each sample. Under specified conditions, we show that the estimation of colony-forming units (CFU), the most common unit of bacterial abundance in classical microbiology, is challenged mostly by resolution and taxon-to-taxon variation. We propose Bayesian cumulative probability models to address such issues. Our results indicate that predictive errors vary consistently below one order of magnitude for total microbial load and abundance of observed bacteria. We also demonstrate our approach has the potential to generalize to previously unseen bacteria, but predictive performance is hampered by specific taxa of uncommon profile. Finally, it remains clear that high-throughput sequencing data are not inherently restricted to sample proportions only, and such technologies bear the potential to meet the working scales of traditional microbiology.

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

BackgroundHuman-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of such effects is limited due to a lack of rapid and scalable assay to comprehensively assess microbiome responses to drugs. Drugs and other compounds can drastically change the overall abundance, taxonomic composition, and functions of a gut microbiome.ResultsHere, we developed an approach to screen compounds against individual microbiomes in vitro, using metaproteomics to both measure absolute bacterial abundances and to functionally profile the microbiome. Our approach was evaluated by testing 43 compounds (including 4 antibiotics) against 5 individual microbiomes. The method generated technically highly reproducible readouts, including changes of overall microbiome abundance, microbiome composition, and functional pathways. Results show that besides the antibiotics, the compounds berberine and ibuprofen inhibited the accumulation of biomass during in vitro growth of the microbiota. By comparing genus and species level-biomass contributions, selective antibacterial-like activities were found with 35 of the 39 non-antibiotic compounds. Seven of the compounds led to a global alteration of the metaproteome, with apparent compound-specific patterns of functional responses. The taxonomic distributions of altered proteins varied among drugs, i.e., different drugs affect functions of different members of the microbiome. We also showed that bacterial function can shift in response to drugs without a change in the abundance of the bacteria.ConclusionsCurrent drug-microbiome interaction studies largely focus on relative microbiome composition and microbial drug metabolism. In contrast, our workflow enables multiple insights into microbiome absolute abundance and functional responses to drugs. The workflow is robust, reproducible, and quantitative and is scalable for personalized high-throughput drug screening applications.

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling.

The use of relative abundance data from next generation sequencing (NGS) can lead to misinterpretations of microbial community structures, as the increase of one taxon leads to the concurrent decrease of the other(s) in compositional data. Although different DNA- and cell-based methods as well as statistical approaches have been developed to overcome the compositionality problem, and the biological relevance of absolute bacterial abundances has been demonstrated, the human microbiome research has not yet adopted these methods, likely due to feasibility issues. Here, we describe how quantitative PCR (qPCR) done in parallel to NGS library preparation provides an accurate estimation of absolute taxon abundances from NGS data and hence provides an attainable solution to compositionality in high-throughput microbiome analyses. The advantages and potential challenges of the method are also discussed.

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.

Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here, we present decomposition of variance using replicate sampling (DIVERS), a method based on replicate sampling and spike-in sequencing. The method quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan's Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance fluctuations at short time scales (weeks), while temporal variability dominated at longer time scales (several months).

Differences in bacterial community structure between three types of biological soil crusts and soil below crusts from the Gurbantunggut Desert, China

The scarcity of knowledge on differences in the microbial assemblage between biological soil crusts (BSCs) and soil below crusts (SBCs) limits our understanding of the contribution of different layers of topsoil to desert ecosystems. This study used Illumina MiSeq sequencing to determine whether differences in bacterial communities among different types of BSCs (algae, lichen and moss dominated) are greater than those between BSCs and their corresponding underlying soils (0–5 cm) in the Gurbantunggut Desert, China. Alpha and beta diversity of bacterial communities showed that richness and diversity were greater in SBCs than in BSCs, but the absolute bacterial abundance was larger in BSCs than in soils. Differences were mainly in the phyla Cyanobacteria, Actinobacteria, Chloroflexi and Acidobacteria. Cyanobacteria were concentrated in BSCs, especially in algae‐dominated BSCs. The relative abundances of Actinobacteria, Chloroflexi and Acidobacteria in SBCs were more than twice those in BSCs, and they were also abundant in the lichen‐ and moss‐dominant crusts. The number of sample‐specific genera was larger in BSCs, but there were more shared genera among SBCs. These results, combined with the principal coordinate analysis and the predicted function profiles, showed that differences in microbial community structure and function in desert ecosystems were greatest between BSCs and the underlying soils, followed by differences among the three types of BSCs, and differences were smallest between the soils below different crusts. These differences might be closely related to the soil chemical properties, especially to pH and fertility. Our study indicated that microbial communities tended to converge in SBCs of different microhabitats.Highlights We studied bacterial community composition in different types of BSCs and SBCs. Differences in bacterial community were greatest between BSCs and SBCs. BSC components contributed to small‐scale microbial heterogeneity in SBCs. Surface soil bacterial communities were strongly stratified even at the centimetre scale from BSCs.

Study protocol on the role of intestinal microbiota in colorectal cancer treatment: a pathway to personalized medicine 2.0

PurposeInvestigate in patients with metastatic and/or irresectable colorectal cancer treated with systemic treatment with capecitabine or TAS-102 whether:Intestinal microbiota composition can act as a predictor for response.Intestinal microbiota composition changes during systemic treatment and its relation to chemotoxicity.BackgroundGut microbiota and host determinants evolve in symbiotic and dependent relationships resulting in a personal ecosystem. In vitro studies showed prolonged and increased response to 5-fluorouracil, a fluoropyrimidine, in the presence of a favorable microbiota composition. Capecitabine and TAS-102 are both fluoropyrimidines used for systemic treatment in colorectal cancer patients.MethodsAn explorative prospective multicenter cohort study in the Maastricht University Medical Centre+ and Zuyderland Medical Centre will be performed in 66 patients. Before, during, and after three cycles of systemic treatment with capecitabine or TAS-102, fecal samples and questionnaires (concerning compliance and chemotoxicity) will be collected. The response will be measured by CT/MRI using RECIST-criteria. Fecal microbiota composition will be analyzed with 16S rRNA next-generation sequencing. The absolute bacterial abundance will be assessed with quantitative polymerase chain reaction. Multivariate analysis will be used for statistical analysis.ConclusionsWe aim to detect a microbiota composition that predicts if patients with metastatic and/or irresectable colorectal cancer will respond to systemic treatment and/or experience zero to limited chemotoxicity. If we are able to identify a favorable microbiota composition, fecal microbiota transplantation might be the low-burden alternative to chemotherapy switch in the future.

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

BackgroundNext-generation 16S ribosomal RNA gene sequencing is widely used to determine the relative composition of the mammalian gut microbiomes. However, in the absence of a reference, this does not reveal alterations in absolute abundance of specific operational taxonomic units if microbial loads vary across specimens.ResultsHere we suggest the spiking of exogenous bacteria into crude specimens to quantify ratios of absolute bacterial abundances. We use the 16S rDNA read counts of the spike-in bacteria to adjust the read counts of endogenous bacteria for changes in total microbial loads. Using a series of dilutions of pooled faecal samples from mice containing defined amounts of the spike-in bacteria Salinibacter ruber, Rhizobium radiobacter and Alicyclobacillus acidiphilus, we demonstrate that spike-in-based calibration to microbial loads allows accurate estimation of ratios of absolute endogenous bacteria abundances. Applied to stool specimens of patients undergoing allogeneic stem cell transplantation, we were able to determine changes in both relative and absolute abundances of various phyla, especially the genus Enterococcus, in response to antibiotic treatment and radio-chemotherapeutic conditioning.ConclusionExogenous spike-in bacteria in gut microbiome studies enable estimation of ratios of absolute OTU abundances, providing novel insights into the structure and the dynamics of intestinal microbiomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0175-0) contains supplementary material, which is available to authorized users.

Natural bacterioplankton assemblage composition during blooms of Alexandrium spp. (Dinophyceae) in NW Mediterranean coastal waters

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 46:55-70 (2007) - doi:10.3354/ame046055 Natural bacterioplankton assemblage composition during blooms of Alexandrium spp. (Dinophyceae) in NW Mediterranean coastal waters Esther Garcés1,2,*, Magda Vila1, Albert Reñé1, Laura Alonso-Sáez1, Silvia Anglès1, Antonella Lugliè2, Mercedes Masó1, Josep M. Gasol1 1Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar—CMIMA, CSIC, Pg. Marítim de la Barceloneta, 37–49, 08003 Barcelona, Spain 2IRTA, Institut de Recerca i Tecnologia Agroalimentaries, Sant Carles de la Ràpita, Spain 3Dipartimento di Botanica ed Ecologia vegetale, University of Sassari, Via Muroni 25, 07100 Sassari, Italy *Email: esther@icm.csic.es ABSTRACT: We characterised the spatial and temporal variation in the bacterioplankton assemblage composition during bloom events of different Alexandrium species (Dinophyceae) in the littoral of the NW Mediterranean Sea by means of catalysed reporter deposition fluorescence in situ hybridisation with oligonucleotide probes (CARD-FISH). We studied several Alexandrium blooms through their seasonal development (at La Fosca beach) or in their spatial variability (in Arenys Harbour and Olbia Bay), and we complemented these observations by describing the composition of the bacterial assemblage associated with cultures of Alexandrium species isolated from the same sites. Our studies on natural bacterioplankton assemblages identified the Bacteroidetes lineage and the Alphaproteobacteria as the dominating components during the studied blooms of Alexandrium. Alphaproteobacteria dominated in the La Fosca and Olbia blooms, while bacteria belonging to the Bacteroidetes were abundant in the development phase of the La Fosca beach bloom and in the winter Arenys bloom. Gammaproteobacteria contributed in low proportions without significant changes through the different bloom phases at La Fosca beach and in Olbia Bay, but were more abundant in Arenys Harbour. While the absolute bacterial abundances in the spatial study of Olbia Bay covaried with the Alexandrium densities, there were no spatial changes in the bacterioplankton assemblage composition. Alteromonas-like organisms were never an important fraction of the assemblage, but Roseobacter dominated Alphaproteobacteria in Arenys Harbour. Furthermore, the bacterioplankton assemblages associated with Alexandrium spp. cultures were very different from the natural bacterial assemblages during blooms of the same species. We conclude that the presence of a given harmful algal bloom species during a bloom will not always necessarily be accompanied by the same bacterial assemblage structure, and studies done with dinoflagellate cultures may only reflect the bacteria capable of growing under laboratory conditions, with little resemblance to what occurs under natural conditions. KEY WORDS: FISH · Dinoflagellates · HAB · Alexandrium · Roseobacter · Alteromonas Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 46, No. 1. Online publication date: January 19, 2007 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2007 Inter-Research.

Bacterial mediation in the utilization of carbon and nitrogen from detrital complexes by Crassostrea virginica

Unattached, cellulolytic bacteria isolated from a salt marsh were cultured on [15N]ammonium sulfate and [14C]glucose and fed to the American oyster Crassostrea virginica. Oysters were able to digest and assimilate bacterial C with an assimilation efficiency of 52.5%. We estimate that free‐living bacteria may be capable of supplying up to ∼9.5% of the total C requirements of oysters in their natural habitat. Cellulolytic bacteria were also cultured on 14C‐labeled refractory Spartina alterniflora particles as the sole C source and [15N]ammonium sulfate as a source of N. These labeled bacteria, together with the S. alterniflora, were fed to the oysters. The refractory C from these detrital complexes was assimilated by the oysters with an efficiency of 10.3%. It was (P= 0.0007) greater than the assimilation efficiency of 2.7% measured in a previous study for oysters feeding on the refractory S. alterniflora substrate alone. This result provides direct experimental evidence that cellulolytic bacteria in the environment can contribute to the transfer of C from refractory detritus to an ecologically important suspension‐feeding macroinvertebrate. We calculated that C. virginica, when fed detrital complexes, assimilated bacterial N with an efficiency of 57.2% but that assimilation of total N present in the detrital complexes was only 3.4%. We speculate that this low assimilation efficiency was due to most (94%) of the N being in the form of condensation products such as humic geopolymers and extracellular polymeric substances secreted by bacteria which could not be digested and absorbed by the oysters. Calculations show that detrital complexes in the natural environment may provide a significant contribution to an oyster’s C demand. The magnitude of this contribution can increase from 1.3 to 60% as both absolute bacterial abundance and proportion of bacteria attached to detrital particles increase, raising the oysters’ efficiency of filtration for these substrates.