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Bibliography on: Microbial Ecology

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ESP: PubMed Auto Bibliography 20 Jul 2019 at 01:41 Created: 

Microbial Ecology

Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

Created with PubMed® Query: "microbial ecology" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-07-19

Zamorano-López N, Borrás L, Giménez JB, et al (2019)

Acclimatised rumen culture for raw microalgae conversion into biogas: Linking microbial community structure and operational parameters in anaerobic membrane bioreactors (AnMBR).

Bioresource technology, 290:121787 pii:S0960-8524(19)31017-X [Epub ahead of print].

Ruminal fluid was inoculated in an Anaerobic Membrane Reactor (AnMBR) to produce biogas from raw Scenedesmus. This work explores the microbial ecology of the system during stable operation at different solids retention times (SRT). The 16S rRNA amplicon analysis revealed that the acclimatised community was mainly composed of Anaerolineaceae, Spirochaetaceae, Lentimicrobiaceae and Cloacimonetes fermentative and hydrolytic members. During the highest biodegradability achieved in the AnMBR (62%) the dominant microorganisms were Fervidobacterium and Methanosaeta. Different microbial community clusters were observed at different SRT conditions. Interestingly, syntrophic bacteria Gelria and Smithella were enhanced after increasing 2-fold the organic loading rate, suggesting their importance in continuous systems producing biogas from raw microalgae.

RevDate: 2019-07-19

Xie M, An F, Wu J, et al (2019)

Meta-omics Reveal Microbial Assortments and Key Enzymes in bean sauce mash, a Traditional Fermented Soybean Product.

Journal of the science of food and agriculture [Epub ahead of print].

BACKGROUND: Dajiang is fermented based on the metabolism of microbial communities in bean sauce mash, a traditional fermented soybean product in China. The current study firstly investigated the metaproteome of bean sauce mash, followed by analyzed biological functions and microbial community to reveal information on strains as well as the expressed proteins to better understand the roles of the microbiota in bean sauce mash.

RESULTS: The metaproteomic results demonstrated that a total of 1415 microbial protein clusters were expressed mainly by members of Penicillium and Rhizopus and were classified into 100 cellular components, 238 biological processes and 220 molecular function categories by GO Annotation. Additionally, enzymes associated with glycolysis metabolic pathways were identified, which can provide the required energy for microbial fermentation. Furthermore, the Illumina MiSeq sequencing technology results showed the microorganism communities of bean sauce mash exhibit a higher diversity, microbiological analysis demonstrated that fungi of Penicillium, Mucor, Fusarium, Aspergillus, Rhizopus, and bacteria of Lactobacillus, Enterococcus, Fructobacillus, Staphylococcus, Carnobacterium, were the predominant genera in 22 samples.

CONCLUSION: The profiles and insights in the current study are important to the research for bean sauce mash and related product in terms of food microbial ecology. Moreover, the strains and information obtained from this study will help the development of sufu starter cultures with unique sensory and stable quality. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-19

Hausmann B, Pjevac P, Huemer M, et al (2019)

Draft Genome Sequence of Desulfosporosinus sp. Strain Sb-LF, Isolated from an Acidic Peatland in Germany.

Microbiology resource announcements, 8(29): pii:8/29/e00428-19.

Desulfosporosinus sp. strain Sb-LF was isolated from an acidic peatland in Bavaria, Germany. Here, we report the draft genome sequence of the sulfate-reducing and lactate-utilizing strain Sb-LF.

RevDate: 2019-07-19

Han P, Yu Y, Zhou L, et al (2019)

Specific Micropollutant Biotransformation Pattern by the Comammox Bacterium Nitrospira inopinata.

Environmental science & technology [Epub ahead of print].

The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.

RevDate: 2019-07-18

Mailloux BJ, Kim C, Kichuk T, et al (2019)

Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer.

Scientific reports, 9(1):10370 pii:10.1038/s41598-019-46663-1.

Determining the carbon sources for active microbial populations in the subsurface is a challenging but highly informative component of subsurface microbial ecology. This work developed a method to provide ecological insights into groundwater microbial communities by characterizing community RNA through its radiocarbon and ribosomal RNA (rRNA) signatures. RNA was chosen as the biomolecule of interest because rRNA constitutes the majority of RNA in prokaryotes, represents recently active organisms, and yields detailed taxonomic information. The method was applied to a groundwater filter collected from a shallow alluvial aquifer in Colorado. RNA was extracted, radiometrically dated, and the 16S rRNA was analyzed by RNA-Seq. The RNA had a radiocarbon signature (Δ14C) of -193.4 ± 5.6‰. Comparison of the RNA radiocarbon signature to those of potential carbon pools in the aquifer indicated that at least 51% of the RNA was derived from autotrophy, in close agreement with the RNA-Seq data, which documented the prevalence of autotrophic taxa, such as Thiobacillus and Gallionellaceae. Overall, this hybrid method for RNA analysis provided cultivation-independent information on the in-situ carbon sources of active subsurface microbes and reinforced the importance of autotrophy and the preferential utilization of dissolved over sedimentary organic matter in alluvial aquifers.

RevDate: 2019-07-17

Ranchou-Peyruse M, Auguet JC, Mazière C, et al (2019)

Geological gas-storage shapes deep life.

Environmental microbiology [Epub ahead of print].

Around the world, several dozen deep sedimentary aquifers are being used for storage of natural gas. Ad-hoc studies of the microbial ecology of some of them have suggested that sulfate-reducing and methanogenic microorganisms play a key role in how these aquifers' communities function. Here, we investigate the influence of gas storage on these two metabolic groups by using high-throughput sequencing and show the importance of sulfate-reducing Desulfotomaculum and a new monophyletic methanogenic group. Aquifer microbial diversity was significantly related to the geological level. The distance to the stored natural gas affects the ratio of sulfate-reducing Firmicutes to deltaproteobacteria. In only one aquifer, the methanogenic archaea dominate the sulfate-reducers. This aquifer was used to store town gas (containing at least 50% H2) around 50 years ago. The observed decrease of sulfates in this aquifer could be related to stimulation of subsurface sulfate-reducers. These results suggest that the composition of the microbial communities is impacted by decades old transient gas storage activity. The tremendous stability of these gas-impacted deep subsurface microbial ecosystems suggests that in situ biotic methanation projects in geological reservoirs may be sustainable over time. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-17

Stres B, L Kronegger (2019)

Shift in the paradigm towards next-generation microbiology.

FEMS microbiology letters pii:5533319 [Epub ahead of print].

In this work, the position of contemporary microbiology is considered from the perspective of scientific success, and a list of historical points and lessons learned from the fields of medical microbiology, microbial ecology and systems biology are presented. In addition, patterns in the development of top-down research topics that emerged over time as well as overlapping ideas and personnel, which are the first signs of trans-domain research activities in the fields of metagenomics, metaproteomics, metatranscriptomics and metabolomics, are explored through analysis of the publication networks of 28.654 papers using the computer programme Pajek. The current state of affairs is defined, and the need for meta-analyses to leverage publication biases in the field of microbiology is put forward as a very important emerging field of microbiology, especially since microbiology is progressively dealing with multiscale systems. Consequently, the need for cross-fertilisation with other fields/disciplines instead of 'more microbiology' is needed to advance the field of microbiology as such. The reader is directed to consider how novel technologies, the introduction of big data approaches and artificial intelligence have transformed microbiology into a multi-scale field and initiated a shift away from its history of mostly manual work and towards a largely technology-, data- and statistics-driven discipline that is often coupled with automation and modelling.

RevDate: 2019-07-17

Paterson JS, Smith RJ, McKerral JC, et al (2019)

A hydrocarbon contaminated aquifer reveals a Piggyback-the-Persistent viral strategy.

FEMS microbiology ecology pii:5533318 [Epub ahead of print].

Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognized fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3-10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.

RevDate: 2019-07-17

Moye ZD, Woolston J, Abbeele PVD, et al (2019)

A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro.

Journal of food protection [Epub ahead of print].

Nontyphoidal Salmonella strains continue to be a major cause of foodborne illness globally. One intriguing approach to reducing the risk of salmonellosis is the direct ingestion of phages targeting Salmonella to enhance natural gut resilience and provide protection during foodborne disease outbreaks. We evaluated the ability of a prophylactically administered bacteriophage cocktail, the foodborne outbreak pill (FOP) targeting Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella, to resolve a Salmonella infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), a simulated gut platform populated by the human intestinal microbiome of healthy donors. The FOP preparation eliminated Salmonella enterica serovar Typhimurium from the colon compartment of the SHIME platform but health-associated metabolites, such as short-chain fatty acids and lactate, remained stable or increased in a donor-dependent manner. In studies of human intestinal cells, pretreatment of Salmonella Typhimurium with the FOP cocktail preserved lipopolysaccharide-stimulated signaling in a Caco-2-THP-1 Transwell system and prevented destruction of the Caco-2 monolayer by Salmonella. Adhesion and invasion of intestinal epithelial cells by Salmonella-a critical factor in Salmonella pathogenesis-was blunted when the bacteria were incubated with the FOP preparation before addition to the monolayer. The FOP phage cocktail was effective for (i) eliminating Salmonella from a simulated human gut without disturbing the indigenous microbiota and (ii) reducing the risk of invasion by Salmonella into the intestinal epithelia. These results suggest that the FOP preparation may be of value for reducing the risk of salmonellosis in humans, e.g., during foodborne disease outbreaks.

RevDate: 2019-07-17

Shih JL, Selph KE, Wall CB, et al (2019)

Trophic Ecology of the Tropical Pacific Sponge Mycale grandis Inferred from Amino Acid Compound-Specific Isotopic Analyses.

Microbial ecology pii:10.1007/s00248-019-01410-x [Epub ahead of print].

Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community. δ15N and δ13C values of amino acids in M. grandis isolated sponge cells are not different from those of its bacterial symbionts. Consequently, there is no difference in trophic position of the sponge and its symbiotic microbes indicating that M. grandis sponge cell isolates do not display amino acid isotopic characteristics typical of metazoan feeding. Furthermore, both the isolated microbial and sponge cell fractions were characterized by a similarly high ΣV value-a measure of bacterial-re-synthesis of organic matter calculated from the sum of variance among individual δ15N values of trophic amino acids. These high ΣV values observed in the sponge suggest that M. grandis is not reliant on translocated photosynthate from photosymbionts or feeding on water column picoplankton, but obtains nutrition through the uptake of amino acids of bacterial origin. Our results suggest that direct assimilation of bacterially synthesized amino acids from its symbionts, either in a manner similar to translocation observed in the coral holobiont or through phagotrophic feeding, is an important if not primary pathway of amino acid acquisition for M. grandis.

RevDate: 2019-07-16

Pantoja-Feliciano IG, Soares JW, Doherty LA, et al (2019)

Acute stressor alters inter-species microbial competition for resistant starch-supplemented medium.

Gut microbes, 10(4):439-446.

Gut microbiome community dynamics are maintained by complex microbe-microbe and microbe-host interactions, which can be disturbed by stress. In vivo studies on the dynamics and manipulation of those interactions are costly and slow, but can be accelerated using in vitro fermentation. Herein, in vitro fermentation was used to determine how an acute stressor, a sudden change in diet, impacts inter-bacterial species competition for resistant starch-supplemented medium (RSM). Fermentation vessels were seeded with fecal samples collected from 10 individuals consuming a habitual diet or U.S. military rations for 21 days. Lactobacillus spp. growth in response to RSM was attenuated following ration consumption, whereas growth of Ruminococcus bromii was enhanced. These differences were not evident in the pre-fermentation samples. Findings demonstrate how incorporating in vitro fermentation into clinical studies can increase understanding of stress-induced changes in nutrient-microbiome dynamics, and suggest that sudden changes in diet may impact inter-species competition for substrates.

RevDate: 2019-07-15

Migliara G, Di Paolo C, Barbato D, et al (2019)

Multimodal surveillance of healthcare associated infections in an intensive care unit of a large teaching hospital.

Annali di igiene : medicina preventiva e di comunita, 31(5):399-413.

BACKGROUND: Healthcare-associated infections (HAIs), or nosocomial infections, represent a significant burden in terms of mortality, morbidity, length of stay and costs for patients hospitalized in intensive care units (ICUs). Surveillance systems are recommended by national and international institutions to gather data on HAIs in order to develop and evaluate interventions that reduce the risk of HAIs.

STUDY DESIGN: ere we describe the methodology and the results of the surveillance system implemented in the ICU of the Policlinico Umberto I, a large teaching hospital in Rome, from April 2016 to October 2018.

METHODS: The multimodal infection surveillance system integrates four different approaches: i) active surveillance of inpatients; ii) environmental microbiological surveillance; iii) surveillance of isolated microorganisms; and iv) behavioral surveillance of healthcare personnel. Data were collected on catheter-related bloodstream infections, ventilation-associated pneumonia, catheter-associated urinary tract infections and primary bloodstream infections that developed in patients after 48 h in the ICU. For environmental surveillance 14 points were selected for sampling (i.e. bed edges, medication carts, PC keyboards, sink faucets). The system of active surveillance of HAIs also included surveillance of microorganisms, consisting of the molecular genotyping of bacterial isolates by pulsed-field gel electrophoresis (PFGE). From 1 November 2016, monitoring of compliance with guidelines for hand hygiene (HH) and proper glove or gown use by healthcare personnel was included in the surveillance system. After the first six months (baseline phase), a multimodal intervention to improve adherence to guidelines by healthcare personnel was conducted with the ICU staff.

RESULTS: Overall, 773 patients were included in the active surveillance. The overall incidence rate of device-related HAIs was 14.1 (95% CI: 12.2-16.3) per 1000 patient-days. The monthly device-related HAI incident rate showed a decreasing trend over time, with peaks of incidence becoming progressively lower. The most common bacterial isolates were Klebsiella pneumoniae (20.7%), Acinetobacter baumannii (17.2%), Pseudomonas aeruginosa (13.4%) and Staphylococcus aureus (5.4%). Acinetobacter baumannii and Klebsiella pneumoniae showed the highest proportion of isolates with a multidrug-resistant profile. A total of 819 environmental samples were collected, from which 305 bacterial isolates were retrieved. The most frequent bacterial isolates were Acinetobacter baumannii (27.2%), Staphylococcus aureus (12.1%), Enterococcus faecalis (11.1%), Klebsiella pneumoniae (5.2%) and Pseudomonas aeruginosa (4.7%). All Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae environmental isolates were at least multidrug-resistant. Genotyping showed a limited number of major PFGE patterns for both clinical and environmental isolates of Klebsiella pneumoniae and Acinetobacter baumannii. Behavioral compliance rates significantly improved from baseline to post-intervention phase.

CONCLUSIONS: By integrating information gathered from active surveillance, environmental microbiological surveillance, surveillance of bacterial isolates and behavioral surveillance of healthcare personnel, the multimodal infection surveillance system returned a precise and detailed view of the infectious risk and microbial ecology of the ICU.

RevDate: 2019-07-15

Garcia-Mazcorro JF, Ishaq SL, Rodriguez-Herrera MV, et al (2019)

Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits.

Animal : an international journal of animal bioscience pii:S1751731119001599 [Epub ahead of print].

All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.

RevDate: 2019-07-15

Houldcroft CJ, Rifkin RF, SJ Underdown (2019)

Human biology and ancient DNA: exploring disease, domestication and movement.

Annals of human biology, 46(2):95-98.

RevDate: 2019-07-13

White JA, Styer A, Rosenwald LC, et al (2019)

Endosymbiotic Bacteria Are Prevalent and Diverse in Agricultural Spiders.

Microbial ecology pii:10.1007/s00248-019-01411-w [Epub ahead of print].

Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence are poorly characterized in many host taxa. Initial surveys have suggested that vertically transmitted symbionts may be particularly common in spiders (Araneae). Here, we used diagnostic PCR and high-throughput sequencing to evaluate symbiont infection in 267 individual spiders representing 14 species (3 families) of agricultural spiders. We found 27 operational taxonomic units (OTUs) that are likely endosymbiotic, including multiple strains of Wolbachia, Rickettsia, and Cardinium, which are all vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Additional strains included Rickettsiella, Spiroplasma, Rhabdochlamydia, and a novel Rickettsiales, all of which could range from pathogenic to mutualistic in their effects upon their hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.

RevDate: 2019-07-12

Mahon BM, Brehony C, Cahill N, et al (2019)

Detection of OXA-48-like-producing Enterobacterales in Irish recreational water.

The Science of the total environment, 690:1-6 pii:S0048-9697(19)33054-2 [Epub ahead of print].

The rapid dissemination of carbapenemase-producing Enterobacterales (CPE) is a major public health concern. The role that the aquatic environment plays in this dissemination is underexplored. This study aimed to examine seawater as a reservoir for CPE. Seawater sampling took place at a bathing site throughout the 2017 bathing season. Each 30 L sample (n = 6) was filtered using the CapE filtration system. Wastewater samples (200 mL) (pre-treatment (n = 3) and post-treatment (n = 3)) were obtained from a nearby secondary wastewater treatment plant, during the same time period. All samples were examined for CPE. Whole genome sequencing of confirmed CPE was carried out using Illumina sequencing. Isolate genomes were hosted in corresponding BIGSdb databases and analyses were performed using multiple web-based tools. CPE was detected in 2/6 seawater samples. It was not detected in any wastewater samples. OXA-48-like-producing ST131 Escherichia coli (Ec_BM707) was isolated from a seawater sample collected in May 2017 and OXA-48-like-producing ST101 Klebsiella pneumoniae (Kp_BM758) was isolated from a seawater sample collected in August 2017. The genomes of the environmental isolates were compared to a collection of previously described Irish clinical OXA-48-like-producing Enterobacterales (n = 105). Ec_BM707 and Kp_BM758 harboured blaOXA-48 on similar mobile genetic elements to those identified in the clinical collection (pOXA-48 fragment in Ec_BM707 and IncL(pOXA-48) plasmid in Kp_BM758). Genetic similarities were observed between Ec_BM707 and several of the clinical ST131 E. coli, with allele matches at up to 98.2% of 2513 core genome multilocus sequence type (cgMLST) loci. In contrast, Kp_BM758 and the 34 clinical K. pneumoniae were genetically distant. The source of the CPE at this site was not identified. The detection of OXA-48-like-producing ST131 E. coli and OXA-48-like-producing ST101 K. pneumoniae in Irish recreational water is a concern. The potential for contamination of the aquatic environment to contribute to dissemination of CPE in Europe warrants further study.

RevDate: 2019-07-12

Mayali X (2019)

NanoSIMS: Microscale Quantification of Biogeochemical Activity with Large-Scale Impacts.

Annual review of marine science [Epub ahead of print].

One major objective of aquatic microbial ecology is to understand the distribution of microbial populations over space and time and in response to environmental factors. Perhaps more importantly, it is crucial to quantify how those microbial cells affect biogeochemical processes of interest, such as primary production, nitrogen cycling, or the breakdown of pollutants. One valuable approach to link microbial identity to activity is to carry out incubations with stable-isotope-labeled substrates and then quantify the isotope incorporation by individual microbial cells using nanoscale secondary ion mass spectrometry (NanoSIMS). This review summarizes recent efforts in this field, highlights novel methods, describes studies investigating rare metabolisms as well as widespread microbial activity, and hopes to provide a framework to increase the use and capabilities of NanoSIMS for microbial biogeochemical studies in the future. Expected final online publication date for the Annual Review of Marine Science Volume 12 is January 3, 2020. Please see for revised estimates.

RevDate: 2019-07-12

Pjevac P, Dyksma S, Goldhammer T, et al (2019)

In situ abundance and carbon fixation activity of distinct anoxygenic phototrophs in the stratified seawater lake Rogoznica.

Environmental microbiology [Epub ahead of print].

Sulfide-driven anoxygenic photosynthesis is an ancient microbial metabolism that contributes significantly to inorganic carbon fixation in stratified, sulfidic water bodies. Methods commonly applied to quantify inorganic carbon fixation by anoxygenic phototrophs, however, cannot resolve the contributions of distinct microbial populations to the overall process. We implemented a straightforward workflow, consisting of radioisotope labeling and flow cytometric cell sorting based on the distinct autofluorescence of bacterial photo pigments, to discriminate and quantify contributions of co-occurring anoxygenic phototrophic populations to in situ inorganic carbon fixation in environmental samples. This allowed us to assign 89.3 ±7.6% of daytime inorganic carbon fixation by anoxygenic phototrophs in Lake Rogoznica (Croatia) to an abundant chemocline-dwelling population of green sulfur bacteria (dominated by Chlorobium phaeobacteroides), whereas the co-occurring purple sulfur bacteria (Halochromatium sp.) contributed only 1.8 ±1.4%. Furthermore, we obtained two metagenome assembled genomes of green sulfur bacteria and one of a purple sulfur bacterium which provides the first genomic insights into the genus Halochromatium, confirming its high metabolic flexibility and physiological potential for mixo- and heterotrophic growth. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-12

Costa FS, Macedo MWFS, Araújo ACM, et al (2019)

Assessing nickel tolerance of bacteria isolated from serpentine soils.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] pii:10.1007/s42770-019-00111-4 [Epub ahead of print].

Serpentine soils present unique characteristics such as a low Ca/Mg ratio, low concentration of nutrients, and a high concentration of heavy metals, especially nickel. Soil bacterial isolates from an ultramafic complex located in the tropical savanna known as the Brazilian Cerrado were studied. Nickel-tolerant bacteria were obtained, and their ability to remove nickel from a culture medium was assessed. Bacterial isolates presented higher tolerance to nickel salts than previously reported for bacteria obtained from serpentine environments in other regions of the world. In addition, the quantification of nickel in cell pellets indicated that at least four isolates may adsorb soluble forms of nickel. It is expected that information gathered in this study will support future efforts to exploit serpentine soil bacteria for biotechnological processes involving nickel decontamination from environmental samples.

RevDate: 2019-07-12

Lajoie G, SW Kembel (2019)

Making the Most of Trait-Based Approaches for Microbial Ecology.

Trends in microbiology pii:S0966-842X(19)30158-1 [Epub ahead of print].

There is an increasing interest in applying trait-based approaches to microbial ecology, but the question of how and why to do it is still lagging behind. By anchoring our discussion of these questions in a framework derived from epistemology, we broaden the scope of trait-based approaches to microbial ecology from one oriented mostly around explanation towards one inclusive of the predictive and integrative potential of these approaches. We use case studies from macro-organismal ecology to concretely show how these goals for knowledge development can be fulfilled and propose clear directions, adapted to the biological reality of microbes, to make the most of recent advancements in the measurement of microbial phenotypes and traits.

RevDate: 2019-07-11

Valverde A, González-Tirante M, Medina-Sierra M, et al (2017)

Culturable bacterial diversity from the chestnut (Castanea sativa Mill.) phyllosphere and antagonism against the fungi causing the chestnut blight and ink diseases.

AIMS microbiology, 3(2):293-314 pii:microbiol-03-02-293.

The phyllosphere supports a large and complex bacterial community that varies both across plant species and geographical locations. Phyllosphere bacteria can have important effects on plant health. The sweet chestnut (Castanea sativa Mill.) is an economically important tree species affected worldwide by the fungal pathogens Cryphonectria parasitica and Phytophthora cinnamomi. We examined the culturable phyllosphere bacterial community of the sweet chestnut at two nearby locations in Central Spain in order to know its geographical variability and to explore its potential as source of biological control agents against these two pathogenic fungi. The bacterial diversity at strain level was high but it varied significantly between locations; however, phylotype richness and diversity were more comparable. The isolates were affiliated with the phyla Actinobacteria, Firmicutes and Proteobacteria. Most of them were members of recognized bacterial species, with a notable proportion of representative of the genera Dietzia and Lonsdalea, but a small fraction of the strains revealed the existence of several potential novel species or even genera. Antagonism tests showed the occurrence in the chestnut phyllosphere of bacterial strains potentially useful as biological control agents against the two pathogenic fungi, some of which belong to species never before described as fungal antagonists. Chestnut phyllosphere, therefore, contains a great diversity of culturable bacteria and may represent an untapped source of potential biocontrol agents against the fungi causing blight and ink diseases of this tree species.

RevDate: 2019-07-11

Defoirdt T (2019)

Amino acid-derived quorum sensing molecules controlling the virulence of vibrios (and beyond).

PLoS pathogens, 15(7):e1007815 pii:PPATHOGENS-D-19-00588.

RevDate: 2019-07-11

Martín-Sánchez L, Singh KS, Avalos M, et al (2019)

Phylogenomic analyses and distribution of terpene synthases among Streptomyces.

Beilstein journal of organic chemistry, 15:1181-1193.

Terpene synthases are widely distributed among microorganisms and have been mainly studied in members of the genus Streptomyces. However, little is known about the distribution and evolution of the genes for terpene synthases. Here, we performed whole-genome based phylogenetic analysis of Streptomyces species, and compared the distribution of terpene synthase genes among them. Overall, our study revealed that ten major types of terpene synthases are present within the genus Streptomyces, namely those for geosmin, 2-methylisoborneol, epi-isozizaene, 7-epi-α-eudesmol, epi-cubenol, caryolan-1-ol, cyclooctat-9-en-7-ol, isoafricanol, pentalenene and α-amorphene. The Streptomyces species divide in three phylogenetic groups based on their whole genomes for which the distribution of the ten terpene synthases was analysed. Geosmin synthases were the most widely distributed and were found to be evolutionary positively selected. Other terpene synthases were found to be specific for one of the three clades or a subclade within the genus Streptomyces. A phylogenetic analysis of the most widely distributed classes of Streptomyces terpene synthases in comparison to the phylogenomic analysis of this genus is discussed.

RevDate: 2019-07-11

Salcher MM, Schaefle D, Kaspar M, et al (2019)

Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae.

The ISME journal pii:10.1038/s41396-019-0471-3 [Epub ahead of print].

The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters ("Ca. Methylopumilus") and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.

RevDate: 2019-07-11

Chuang JS, Frentz Z, S Leibler (2019)

Homeorhesis and ecological succession quantified in synthetic microbial ecosystems.

Proceedings of the National Academy of Sciences of the United States of America pii:1901055116 [Epub ahead of print].

The dynamics of ecological change following a major perturbation, known as succession, are influenced by random processes. Direct quantitation of the degree of contingency in succession requires chronological study of replicate ecosystems. We previously found that population dynamics in carefully controlled, replicated synthetic microbial ecosystems were strongly deterministic over several months. Here, we present simplified, two-species microbial ecosystems consisting of algae and ciliates, imaged in toto at single-cell resolution with fluorescence microscopy over a period of 1 to 2 weeks. To directly study succession in these ecosystems, we deliberately varied the initial cell abundances over replicates and quantified the ensuing dynamics. The distribution of abundance trajectories rapidly converged to a nearly deterministic path, with small fluctuations, despite variations in initial conditions, environmental perturbations, and intrinsic noise, indicative of homeorhesis. Homeorhesis was also observed for certain phenotypic variables, such as partitioning of the ciliates into distinct size classes and clumping of the algae. Although the mechanism of homeorhesis observed in these synthetic ecosystems remains to be elucidated, it is clear that it must emerge from the ways each species controls its own internal states, with respect to a diverse set of environmental conditions and ecological interactions.

RevDate: 2019-07-11

Moeller AH, Gomes-Neto JC, Mantz S, et al (2019)

Experimental Evidence for Adaptation to Species-Specific Gut Microbiota in House Mice.

mSphere, 4(4): pii:4/4/e00387-19.

The gut microbial communities of mammals have codiversified with host species, and changes in the gut microbiota can have profound effects on host fitness. Therefore, the gut microbiota may drive adaptation in mammalian species, but this possibility is underexplored. Here, we show that the gut microbiota has codiversified with mice in the genus Mus over the past ∼6 million years, and we present experimental evidence that the gut microbiota has driven adaptive evolution of the house mouse, Mus musculusdomesticus Phylogenetic analyses of metagenome-assembled bacterial genomic sequences revealed that gut bacterial lineages have been retained within and diversified alongside Mus species over evolutionary time. Transplantation of gut microbiotas from various Mus species into germfree M. m. domesticus showed that foreign gut microbiotas slowed growth rate and upregulated macrophage inflammatory protein in hosts. These results suggest adaptation by M. m. domesticus to its gut microbiota since it diverged from other Mus species.IMPORTANCE The communities of bacteria that reside within mammalian guts are deeply integrated with their hosts, but the impact of this gut microbiota on mammalian evolution remains poorly understood. Experimental transplantation of the gut microbiota between mouse species revealed that foreign gut microbiotas lowered the host growth rate and upregulated the expression of an immunomodulating cytokine. In addition, foreign gut microbiotas increased host liver sizes and attenuated sex-specific differences in host muscle and fat content. These results suggest that the house mouse has adapted to its species-specific gut microbiota.

RevDate: 2019-07-11

Schmidt R, Ulanova D, Wick LY, et al (2019)

Microbe-driven chemical ecology: past, present and future.

The ISME journal pii:10.1038/s41396-019-0469-x [Epub ahead of print].

In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.

RevDate: 2019-07-10

De Tender C, Mesuere B, Van der Jeugt F, et al (2019)

Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome.

Scientific reports, 9(1):9890 pii:10.1038/s41598-019-46106-x.

Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.

RevDate: 2019-07-09

Meola M, Rifa E, Shani N, et al (2019)

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.

BMC genomics, 20(1):560 pii:10.1186/s12864-019-5914-8.

BACKGROUND: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.

RESULTS: We provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis ( The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.

RevDate: 2019-07-09

Puentes-Téllez PE, JF Salles (2019)

Dynamics of Abundant and Rare Bacteria During Degradation of Lignocellulose from Sugarcane Biomass.

Microbial ecology pii:10.1007/s00248-019-01403-w [Epub ahead of print].

Microorganisms play a crucial role in lignocellulosic degradation. Many enriched microbial communities have demonstrated to reach functional and structural stability with effective degrading capacities of industrial interest. These microbial communities are typically composed by only few dominant species and a high number of usually overlooked rare species. Here, we used two sources of lignocellulose (sugarcane bagasse and straw) in order to obtain lignocellulose-degrading bacteria through an enriched process, followed the selective trajectory of both abundant and rare bacterial communities by 16S rRNA gene amplification and analyzed the outcomes of selection in terms of capacities and specialization. We verified the importance of pre-selection by using two sources of microbial inoculum: soil samples from a sugarcane field with history of straw addition (St15) and control samples, from the same field, without amendments (St0). We found similitudes in terms of stabilization between the abundant and rare fractions. We also found positive correlations of both abundant and rare taxa (like Caulobacteraceae and Alcaligenaceae) and the degradation of lignocellulosic fractions. Differences in the inocula's initial diversity rapidly decreased during the enrichment resulting in comparable richness levels at the end of the process; however, the legacy of the St15 inoculum and its specialization positively influenced the degradation capacities of the community. Analysis of specialization of the final communities revealed increased straw degradation capacity in the communities enriched in bagasse, which could be potentially used as a strategy for improving lignocellulose waste degradation on the sugarcane fields. This work highlights the importance of including the rare fraction of bacterial communities during investigations involving the screening and assessment of effective degrading communities.

RevDate: 2019-07-09

Cutler NA, Arróniz-Crespo M, Street LE, et al (2019)

Correction to: Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance.

The original version of this article contained an error in the Molecular Analysis subsection of the Methods.

RevDate: 2019-07-09

Johnston ER, Hatt JK, He Z, et al (2019)

Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.

Proceedings of the National Academy of Sciences of the United States of America pii:1901307116 [Epub ahead of print].

Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.

RevDate: 2019-07-09

Greenlon A, Chang PL, Damtew ZM, et al (2019)

Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.

Proceedings of the National Academy of Sciences of the United States of America pii:1900056116 [Epub ahead of print].

Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.

RevDate: 2019-07-09

Wörner S, M Pester (2019)

The microbial succession of anaerobic chitin degradation in freshwater sediments.

Applied and environmental microbiology pii:AEM.00963-19 [Epub ahead of print].

Chitin is massively produced by freshwater plankton species as structural element of their exoskeleton or cell wall. At the same time, chitin does not accumulate in the pre-dominantly anoxic sediments, underlining its importance as carbon and nitrogen source for sedimentary microorganisms. We studied chitin degradation in littoral sediment of Lake Constance as Central Europe's third largest lake. Turnover of the chitin analog methyl-umbelliferyl-N,N-diacetylchitobioside (MUF-DC) was highest in the upper oxic sediment layer with 5.4 nmol MUF-DC h-1 (g sediment dry weight)-1 In the underlying anoxic sediment layers, chitin hydrolysis decreased with depth from 1.1 to 0.08 nmol MUF-DC h-1 (g sediment dry weight)-1 Bacteria involved in chitin degradation were identified by 16S rRNA (gene) amplicon sequencing of anoxic microcosms incubated in the presence of chitin as compared to microcosms amended either with N-acetylglucosamine as the monomer of chitin or no substrate. Chitin degradation was driven by a succession of bacteria responding specifically to chitin only. The early phase (0-9 days) was dominated by Chitinivibrio spp. (Fibrobacteres). The intermediate phase (9-21 days) was characterized by a higher diversity of chitin responders, including besides Chitinivibrio spp. also members of the phyla Bacteroidetes, Proteobacteria, Spirochaetes, and Chloroflexi In the late phase (21-43 days), the Chitinivibrio populations broke down at a parallel strong increase of Ruminiclostridium spp. (formerly Clostridium cluster III, Firmicutes), which became the dominating chitin responders. Our study provides quantitative insights into anaerobic chitin degradation in lake sediments and linked this to a model of microbial succession associated with this activity.Importance Chitin is the most abundant biopolymer in aquatic environments with direct impact on the carbon and nitrogen cycles. Despite its massive production as structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in pre-dominantly anoxic freshwater sediments and the responsible microorganisms. We could prove that chitin is readily degraded under anoxic conditions and link this to a succession of the responsible microbial community over a 43 days period. While Fibrobacteres and Firmicutes members were driving the early and late phase of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded towards the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.

RevDate: 2019-07-10

Lorenz C, Roscher L, Meyer MS, et al (2019)

Spatial distribution of microplastics in sediments and surface waters of the southern North Sea.

Environmental pollution (Barking, Essex : 1987), 252(Pt B):1719-1729 pii:S0269-7491(19)31854-8 [Epub ahead of print].

Microplastic pollution within the marine environment is of pressing concern globally. Accordingly, spatial monitoring of microplastic concentrations, composition and size distribution may help to identify sources and entry pathways, and hence allow initiating focused mitigation. Spatial distribution patterns of microplastics were investigated in two compartments of the southern North Sea by collecting sublittoral sediment and surface water samples from 24 stations. Large microplastics (500-5000 μm) were detected visually and identified using attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. The remaining sample was digested enzymatically, concentrated onto filters and analyzed for small microplastics (11-500 μm) using Focal Plane Array (FPA) FTIR imaging. Microplastics were detected in all samples with concentrations ranging between 2.8 and 1188.8 particles kg-1 for sediments and 0.1-245.4 particles m-3 for surface waters. On average 98% of microplastics were <100 μm in sediments and 86% in surface waters. The most prevalent polymer types in both compartments were polypropylene, acrylates/polyurethane/varnish, and polyamide. However, polymer composition differed significantly between sediment and surface water samples as well as between the Frisian Islands and the English Channel sites. These results show that microplastics are not evenly distributed, in neither location nor size, which is illuminating regarding the development of monitoring protocols.

RevDate: 2019-07-08

Philip N, Leishman SJ, Bandara HMHN, et al (2019)

Randomized Controlled Study to Evaluate Microbial Ecological Effects of CPP-ACP and Cranberry on Dental Plaque.

JDR clinical and translational research [Epub ahead of print].

INTRODUCTION: Ecological approaches to dental caries prevention play a key role in attaining long-term control over the disease and maintaining a symbiotic oral microbiome.

OBJECTIVES: This study aimed to investigate the microbial ecological effects of 2 interventional dentifrices: a casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) dentifrice and the same dentifrice supplemented with a polyphenol-rich cranberry extract.

METHODS: The interventional toothpastes were compared with each other and with an active control fluoride dentifrice in a double-blinded randomized controlled trial. Real-time quantitative polymerase chain reaction (qPCR) analysis was used to determine changes in the bacterial loads of 14 key bacterial species (8 caries associated and 6 health associated) in the dental plaque of trial participants after they used the dentifrices for 5 to 6 wk.

RESULTS: From the baseline to the recall visit, significant differences were observed between the treatment groups in the bacterial loads of 2 caries-associated bacterial species (Streptococcus mutans [P < 0.001] and Veillonella parvula [P < 0.001]) and 3 health-associated bacterial species (Corynebacterium durum [P = 0.008], Neisseria flavescens [P = 0.005], and Streptococcus sanguinis [P < 0.001]). Compared to the fluoride control dentifrice, the CPP-ACP dentifrice demonstrated significant differences for S. mutans (P = 0.032), C. durum (P = 0.007), and S. sanguinis (P < 0.001), while combination CPP-ACP-cranberry dentifrice showed significant differences for S. mutans (P < 0.001), V. parvula (P < 0.001), N. flavescens (P = 0.003), and S. sanguinis (P < 0.001). However, no significant differences were observed in the bacterial load comparisons between the CPP-ACP and combination dentifrices for any of the targeted bacterial species (P > 0.05).

CONCLUSIONS: Overall, the results indicate that dentifrices containing CPP-ACP and polyphenol-rich cranberry extracts can influence a species-level shift in the ecology of the oral microbiome, resulting in a microbial community less associated with dental caries (Australian New Zealand Clinical Trial Registry ANZCTR 12618000095268).

KNOWLEDGE TRANSFER STATEMENT: The results of this randomized controlled trial indicate that dentifrices containing casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) and polyphenol-rich cranberry extracts were able to beneficially modulate the microbial ecology of dental plaque in a group of high caries-risk patients. This could contribute toward lowering the risk of developing new caries lesions, an important goal sought by patients, clinicians, and policy makers.

RevDate: 2019-07-07

Ghosh A, P Bhadury (2019)

Vibrio chemaguriensis sp. nov., from Sundarbans, Bay of Bengal.

Current microbiology pii:10.1007/s00284-019-01731-7 [Epub ahead of print].

A new species of Vibrio (annotated as SBOTS_Iso1) was isolated in August 2014 from the Stn1 located in Chemaguri creek of Sundarbans mangrove ecoregion and taxonomically characterized using a polyphasic approach. Phenotypic analysis including biochemical tests and growth across a wide range of salinities indicated the typical estuarine characteristics of this new species. The bacterium was Gram negative, rod-shaped, oxidase and catalase negative and grows in the presence of NaCl. FAME analysis indicated 31.7% of the cellular fatty acids to be made up of 16:1 ω7c/16:1 ω6c. Amplification and sequencing of 16S rRNA and multilocus sequence analysis of four loci (2040 bp; rpoA, topA, mreB, pyrH) and additional sequence data of ftsZ, atpD, ompW and rpoB genes showed this isolate to be a member of Harveyi clade of the genus Vibrio. The closest phylogenetic neighbour was Vibrio alginolyticus ATCC 17749T with 96.8% similarity. Whole-genome sequence data indicates the presence of ~ 5 Mbp genome. GGDC, orthoANIu and AAI indicated 45%, 92% and 0.962 identity respectively with genome of Vibrio alginolyticus ATCC 17749T. The isolate SBOTS_Iso1 has been named Vibrio chemaguriensis sp. nov. on the name of the site from where it was first isolated.

RevDate: 2019-07-07

Chen H, Li C, Liu T, et al (2019)

A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species.

Microbial ecology pii:10.1007/s00248-019-01409-4 [Epub ahead of print].

Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution.

RevDate: 2019-07-06

Gros M, Marti E, Balcázar JL, et al (2019)

Fate of pharmaceuticals and antibiotic resistance genes in a full-scale on-farm livestock waste treatment plant.

Journal of hazardous materials, 378:120716 pii:S0304-3894(19)30659-4 [Epub ahead of print].

This study investigated, for the first time, the distribution and fate of 28 multiple-class veterinary pharmaceuticals and antibiotics (PhACs), and their corresponding antibiotic resistance genes (ARGs), in a full-scale on-farm livestock waste treatment plant. The plant relies on several technologies, including: anaerobic digestion (AD), solid-liquid separation, and two stages reverse osmosis (RO) of the liquid digestate. Tetracycline, fluoroquinolone, lincosamide and pleuromutilin antibiotics, together with anti-helmintic (flubendazole) and anti-inflammatory (flunixin) drugs were the most frequently detected compounds in livestock waste and in slaughterhouse sludge. This last fraction is used as co-substrate in the AD process and showed to be an important input source of PhACs and ARGs. In terms of treatment performance, AD exhibited moderate to low PhACs and ARGs reduction, while a large fraction (<50%) of the PhACs present in the digestate were distributed onto the solid fraction, after solid-liquid separation. Both solid and liquid digestates had relatively high copy numbers of ARGs. Finally, RO showed high rejection percentages for all PhACs (<90%), with concentrations in the low ng L-1 range in permeates, for most target PhACs. Nevertheless, moderate copy numbers of ARGs were detected in permeates.

RevDate: 2019-07-05

Lukumbuzya M, Schmid M, Pjevac P, et al (2019)

A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms.

Frontiers in microbiology, 10:1383.

Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a key method for the detection of (uncultured) microorganisms in environmental and medical samples. A major limitation of standard FISH protocols, however, is the small number of phylogenetically distinct target organisms that can be detected simultaneously. In this study, we introduce a multicolor FISH approach that uses eight fluorophores with distinct spectral properties, which can unambiguously be distinguished by confocal laser scanning microscopy combined with white light laser technology. Hybridization of rRNA-targeted DNA oligonucleotide probes, which were mono-labeled with these fluorophores, to Escherichia coli cultures confirmed that the fluorophores did not affect probe melting behavior. Application of the new multicolor FISH method enabled the differentiation of seven (potentially up to eight) phylogenetically distinct microbial populations in an artificial community of mixed pure cultures (five bacteria, one archaeon, and one yeast strain) and in activated sludge from a full-scale wastewater treatment plant. In contrast to previously published multicolor FISH approaches, this method does not rely on combinatorial labeling of the same microorganisms with different fluorophores, which is prone to biases. Furthermore, images acquired by this method do not require elaborate post-processing prior to analysis. We also demonstrate that the newly developed multicolor FISH method is compatible with an improved cell fixation protocol for FISH targeting Gram-negative bacterial populations. This fixation approach uses agarose embedding during formaldehyde fixation to better preserve the three-dimensional structure of spatially complex samples such as biofilms and activated sludge flocs. The new multicolor FISH approach should be highly suitable for studying structural and functional aspects of microbial communities in virtually all types of samples that can be analyzed by conventional FISH methods.

RevDate: 2019-07-05

Kerfahi D, Ogwu MC, Ariunzaya D, et al (2019)

Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils.

Microbial ecology pii:10.1007/s00248-019-01405-8 [Epub ahead of print].

The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the "normal" community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs. The fungal community in the sites with high metal concentrations is no less diverse than that in areas with normal background levels. Overall, these findings raise interesting questions of the evolutionary origin and functional characteristics of this apparently "metal-tolerant" community, and of the associated soil biota in general. It is possible that rehabilitation of metal-contaminated mined soils from spoil heaps could benefit from the incorporation of fungi derived from these areas.

RevDate: 2019-07-05

Pant A, Das B, RK Bhadra (2019)

CTX phage of Vibrio cholerae: Genomics and applications.

Vaccine pii:S0264-410X(19)30796-0 [Epub ahead of print].

The bipartite genome of Vibrio cholerae is divided into two circular non-homologous chromosomes, which harbor several genetic elements like phages, plasmids, transposons, integrative conjugative elements, and pathogenic islands that encode functions responsible for disease development, antimicrobial resistance, and subsistence in hostile environments. These elements are highly heterogeneous, mobile in nature, and encode their own mobility functions or exploit host-encoded enzymes for intra- and inter-cellular movements. The key toxin of V. cholerae responsible for the life-threatening diarrheal disease cholera, the cholera toxin, is coded by part of the genome of a filamentous phage, CTXϕ. The replicative genome of CTXϕ is divided into two distinct modular structures and has adopted a unique strategy for its irreversible integration into the V. cholerae chromosomes. CTXϕ exploits two host-encoded tyrosine recombinases, XerC and XerD, for its integration in the highly conserved dimer resolution site (dif) of V. cholerae chromosomes. CTXϕ can replicate only in the limited number of Vibrio species. In contrast, the phage integration into the bacterial chromosome does not rely on its replication and could integrate to the dif site of large numbers of gram-negative bacteria. Recent pangenomic analysis revealed that like CTXϕ, the bacterial dif site is the integration spot for several other mobile genetic elements such as plasmids and genomic islands. In this review we discuss about current molecular insights into CTXϕ genomics and its replication and integration mechanisms into hosts. Particular emphasis has been given on the exploitation of CTXϕ genomics knowledge in developing genetic tools and designing environmentally safe recombinant live oral cholera vaccine strains.

RevDate: 2019-07-05

Das B, Verma J, Kumar P, et al (2019)

Antibiotic resistance in Vibrio cholerae: Understanding the ecology of resistance genes and mechanisms.

Vaccine pii:S0264-410X(19)30793-5 [Epub ahead of print].

The unique genetic makeup and remarkable competency of Vibrio cholerae are the key factors that help the cholera pathogen adapt rapidly to adverse environmental conditions and resist the detrimental effect of antimicrobial agents. In the last few decades, V. cholerae that causes acute watery diarrhoeal disease cholera has emerged as a notorious multidrug resistant (MDR) enteric pathogen. Although chromosomal mutations can contribute to antimicrobial resistance (AMR), the frequent acquisition of extrachromosomal mobile genetic elements (MGEs) from closely/distantly related bacterial species are major players in V. cholerae drug resistance. Whole genome sequence analysis of clinical and environmental V. cholerae strains revealed that the genome of most of the recent isolates harbour integrating conjugative elements (ICEs), plasmids, superintegron, transposable elements and insertion sequences, which are the key carriers of genetic traits encoding antimicrobial resistance function. Different antimicrobial resistance genes identified in V. cholerae can contribute in antibiotic resistance by facilitating one of the following three mechanisms; (i) reduced permeability or active efflux of the antibiotics, (ii) alteration of the antibiotic targets by introducing post-transcriptional/translational modifications and (iii) hydrolysis or chemical modification of antibiotics. Here, we present an overview of the present insights on the emergence and mechanisms of AMR in V. cholerae.

RevDate: 2019-07-04

Moeller FU, Webster NS, Herbold CW, et al (2019)

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta.

Environmental microbiology [Epub ahead of print].

Marine sponges represent one of the few eukaryotic groups that frequently harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. "Candidatus Nitrosospongia ianthellae" is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbor nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals. This article is protected by copyright. All rights reserved.

RevDate: 2019-07-04

Dann LM, Clanahan M, Paterson JS, et al (2019)

Distinct niche partitioning of marine and freshwater microbes during colonisation.

FEMS microbiology ecology pii:5528309 [Epub ahead of print].

Bacteria are ubiquitous on Earth, and many use chemotaxis to colonise favourable microenvironments. The colonisation process is continuous, where animals, plants, protists, viruses, chemical and physical factors frequently remove bacteria from wide volume ranges. Colonisation processes are poorly understood in natural communities. Here, we investigated niche partitioning during colonisation in aquatic microbial communities using bands of bacterial chemotaxis in petri dishes from mixed-species communities. The community partitioned into loiterers, primary and secondary colonisers, each having distinct abundances and taxonomy. Within marine samples, Shewanella dominated the primary colonisers, whilst Enterobacteriaceae dominated this group within the freshwater samples. Whether the success of these specific groups translates to what occurs within natural communities is uncertain but here we show these taxa have the capacity to colonise new, unexplored environments. A strong negative association existed between the primary colonisers and viral abundance, suggesting successful colonisers simultaneously move toward areas of heightened resources, which correlated with lower virus-like particles. Here, we show microbial communities constantly sort themselves into distinct taxonomic groups as they move into new environments. This sorting during colonisation may be fundamental to microbial ecology, industry, technology and disease development by setting the initial conditions that determine the winners as a community develops.

RevDate: 2019-07-03

Stirling E, Macdonald LM, Smernik RJ, et al (2019)

Soil Microbial Community Responses After Amendment with Thermally Altered Pinus radiata Needles.

Microbial ecology pii:10.1007/s00248-019-01402-x [Epub ahead of print].

Post-fire litter layers are composed of leaves and woody debris that predominantly fall during or soon after the fire event. These layers are distinctly different to pre-fire litters due to their common origin and deposition time. However, heterogeneity can arise from the variable thermal conditions in the canopy during fire. Therefore, in this study, we used thermally altered pine needles (heated to 40 °C, 150 °C, 260 °C and 320 °C for 1 h) in a laboratory incubation study for 43 days. These samples were measured for respiration throughout and extracted for DNA at the experiment's end; soil ribosomal RNA was analysed using Illumina sequencing (16S and internal transcribed spacer amplicons). The addition of pine needles heated to 40 °C or 150 °C caused a substantial shift in community structure, decreased alpha diversity and significantly increased soil respiration relative to the control treatment. In contrast, pine needles heated to 260 °C or 320 °C had little effect on microbial community structure or soil respiration. These results indicate that highly thermally altered needles are not microbially decomposed during the first 43 days of exposure and therefore that biomass temperature may have significant effects on post-fire litter decomposition and carbon flux. This research outlines an important knowledge gap in forest fire responses that may affect post-fire carbon emission estimates.

RevDate: 2019-07-03

Ou L, Qin X, Shi X, et al (2019)

Alkaline phosphatase activities and regulation in three harmful Prorocentrum species from the coastal waters of the East China Sea.

Microbial ecology pii:10.1007/s00248-019-01399-3 [Epub ahead of print].

Harmful blooms of Prorocentrum donghaiense occur annually in the phosphorus-scarce coastal waters of the East China Sea (ECS). The enzymatic activities of alkaline phosphatase (AP) and its regulation by external phosphorus were studied during a P. donghaiense bloom in this area. The AP characteristics of P. donghaiense was further compared with Prorocentrum minimum and Prorocentrum micans in monocultures with both bulk and single-cell enzyme-labeled fluorescence AP assays. Concentrations of dissolved inorganic phosphorus (DIP) varied between 0.04 and 0.73 μmol l-1, with more than half recording stations registering concentrations below 0.10 μmol l-1. Concentrations of dissolved organic phosphorus (DOP) were comparable or even higher than those of DIP. P. donghaiense suffered phosphorus stress and expressed abundant AP, especially when DIP was lower than 0.10 μmol l-1. The AP activities showed a negative correlation with DIP but a positive correlation with DOP. The AP activities were also regulated by internal phosphorus pool. The sharp increase in AP activities was observed until cellular phosphorus was exhausted. Most AP of P. donghaiense was located on the cell surface and some were released into the water with time. Compared with P. minimum and P. micans, P. donghaiense showed a higher AP affinity for organic phosphorus substrates, a more efficient and energy-saving AP expression quantity as a response to phosphorus deficiency. The unique AP characteristic of P. donghaiense suggests that it benefits from the efficient utilization of DOP, and outcompete other species in the phosphorus-scarce ECS.

RevDate: 2019-07-03

Grunert O, Robles-Aguilar AA, Hernandez-Sanabria E, et al (2019)

Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media.

Scientific reports, 9(1):9561 pii:10.1038/s41598-019-45290-0.

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

RevDate: 2019-07-03

Sze MA, Topçuoğlu BD, Lesniak NA, et al (2019)

Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure.

mBio, 10(4): pii:mBio.01454-19.

Colonic bacterial populations are thought to have a role in the development of colorectal cancer with some protecting against inflammation and others exacerbating inflammation. Short-chain fatty acids (SCFAs) have been shown to have anti-inflammatory properties and are produced in large quantities by colonic bacteria that produce SCFAs by fermenting fiber. We assessed whether there was an association between fecal SCFA concentrations and the presence of colonic adenomas or carcinomas in a cohort of individuals using 16S rRNA gene and metagenomic shotgun sequence data. We measured the fecal concentrations of acetate, propionate, and butyrate within the cohort and found that there were no significant associations between SCFA concentration and tumor status. When we incorporated these concentrations into random forest classification models trained to differentiate between people with healthy colons and those with adenomas or carcinomas, we found that they did not significantly improve the ability of 16S rRNA gene or metagenomic gene sequence-based models to classify individuals. Finally, we generated random forest regression models trained to predict the concentration of each SCFA based on 16S rRNA gene or metagenomic gene sequence data from the same samples. These models performed poorly and were able to explain at most 14% of the observed variation in the SCFA concentrations. These results support the broader epidemiological data that questions the value of fiber consumption for reducing the risks of colorectal cancer. Although other bacterial metabolites may serve as biomarkers to detect adenomas or carcinomas, fecal SCFA concentrations have limited predictive power.IMPORTANCE Considering that colorectal cancer is the third leading cancer-related cause of death within the United States, it is important to detect colorectal tumors early and to prevent the formation of tumors. Short-chain fatty acids (SCFAs) are often used as a surrogate for measuring gut health and for being anticarcinogenic because of their anti-inflammatory properties. We evaluated the fecal SCFA concentrations of a cohort of individuals with different colonic tumor burdens who were previously analyzed to identify microbiome-based biomarkers of tumors. We were unable to find an association between SCFA concentration and tumor burden or use SCFAs to improve our microbiome-based models of classifying people based on their tumor status. Furthermore, we were unable to find an association between the fecal community structure and SCFA concentrations. Our results indicate that the association between fecal SCFAs, the gut microbiome, and tumor burden is weak.

RevDate: 2019-07-02

de Boer W, Li X, Meisner A, et al (2019)

Pathogen suppression by microbial volatile organic compounds in soils.

FEMS microbiology ecology pii:5527321 [Epub ahead of print].

There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers extrapolation of production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures, do also occur in soil atmospheres. Therefore, integration of lab and field studies on production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with knowledge on chemistry and physical behaviour of mVOCs in soils, forms the basis for development of sustainable management strategies to enhance natural control of soil-borne pathogens with mVOCs. Possibilities for mVOCs-based control of soil-borne pathogens are discussed.

RevDate: 2019-07-02

Yi Y, Wang H, Chen Y, et al (2019)

Identification of Novel Butyrate- and Acetate-Oxidizing Bacteria in Butyrate-Fed Mesophilic Anaerobic Chemostats by DNA-Based Stable Isotope Probing.

Microbial ecology pii:10.1007/s00248-019-01400-z [Epub ahead of print].

Butyrate is one of the most important intermediates during anaerobic digestion of protein wastewater, and its oxidization is considered as a rate-limiting step during methane production. However, information on syntrophic butyrate-oxidizing bacteria (SBOB) is limited due to the difficulty in isolation of pure cultures. In this study, two anaerobic chemostats fed with butyrate as the sole carbon source were operated at different dilution rates (0.01/day and 0.05/day). Butyrate- and acetate-oxidizing bacteria in both chemostats were investigated, combining DNA-Stable Isotope Probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results showed that, in addition to known SBOB, Syntrophomonas, other species of unclassified Syntrophomonadaceae were putative butyrate-oxidizing bacteria. Species of Mesotoga, Aminivibrio, Acetivibrio, Desulfovibrio, Petrimonas, Sedimentibacter, unclassified Anaerolineae, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria may contribute to acetate oxidation from butyrate metabolism. Among them, the ability of butyrate oxidation was unclear for species of Sedimentibacter, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria. These results suggested that more unknown species participated in the degradation of butyrate. However, the corresponding function and pathway for butyrate or acetate oxidization of these labeled species need to be further investigated.

RevDate: 2019-07-02

Song HS, Lee JY, Haruta S, et al (2019)

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities.

Frontiers in microbiology, 10:1264.

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that - in many cases - adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future.

RevDate: 2019-07-02

Ganin H, Kemper N, Meir S, et al (2019)

Indole Derivatives Maintain the Status Quo Between Beneficial Biofilms and Their Plant Hosts.

Molecular plant-microbe interactions : MPMI [Epub ahead of print].

Biofilms formed by bacteria on plant roots play an important role in maintaining an optimal rhizosphere environment that supports plant growth and fitness. Bacillus subtilis is a potent plant growth promoter, forming biofilms that play a key role in protecting the host from fungal and bacterial infections. In this work, we demonstrate that the development of B. subtilis biofilms is antagonized by specific indole derivatives that accumulate during symbiotic interactions with plant hosts. Indole derivatives are more potent signals when the plant polysaccharide xylan serves as a carbon source, a mechanism to sustain beneficial biofilms at a biomass that can be supported by the plant. Moreover, B. subtilis biofilms formed by mutants resistant to indole derivatives become deleterious to the plants due to their capacity to consume and recycle plant polysaccharides. These results demonstrate how a dynamic metabolite-based dialogue can promote homeostasis between plant hosts and their beneficial biofilm communities.

RevDate: 2019-07-01

Hu K, Tao JP, He DN, et al (2019)

[Effects of root growth on dynamics of microbes and enzyme activities during litter decomposition.].

Ying yong sheng tai xue bao = The journal of applied ecology, 30(6):1993-2001.

To understand the influence of roots of understory plant entering litter layer on litter decomposition in forest ecosystems, we examined the effects of different treatments of Lolium multiflorum root biomass on microorganisms and enzyme activities during leaf litter decomposition of Symplocos setchuensis, a dominant species in a mid-subtropical evergreen broad-leaved forest, through a litter bag simulation experiment. Results showed that diversity index of bacterial and fungal communities of leaf litter surface under three treatments, i.e. no root (N), less roots (L), more roots (M), in a 240-day decomposition process showed the following pattern: M > L > N. The effects of these different root biomass treatments on the composition and quantity of fungal community were more significant than those on bacterial community. The biomass of living roots growing in the litter bag gradually decreased at the end of the growing season of L. multiflorum. The impacts of root growth on the composition of the fungal community gradually decreased during decomposition. At the same decomposition stage, the activities of acid phosphatase, β-glucosidase, polyphenol oxidase, and peroxidase on the litter surface were higher in the treatments with roots than that without roots. These results indicated that root growth could change the composition and quantity of microbial communities and increase the extracellular enzyme activities of microbes, and thus stimulating litter decomposition.

RevDate: 2019-06-29

Carr A, Diener C, Baliga NS, et al (2019)

Use and abuse of correlation analyses in microbial ecology.

The ISME journal pii:10.1038/s41396-019-0459-z [Epub ahead of print].

Correlation analyses are often included in bioinformatic pipelines as methods for inferring taxon-taxon interactions. In this perspective, we highlight the pitfalls of inferring interactions from covariance and suggest methods, study design considerations, and additional data types for improving high-throughput interaction inferences. We conclude that correlation, even when augmented by other data types, almost never provides reliable information on direct biotic interactions in real-world ecosystems. These bioinformatically inferred associations are useful for reducing the number of potential hypotheses that we might test, but will never preclude the necessity for experimental validation.

RevDate: 2019-06-28

Callewaert C, Nakatsuji T, Knight R, et al (2019)

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis.

The Journal of investigative dermatology pii:S0022-202X(19)31789-0 [Epub ahead of print].

Dupilumab is a fully human antibody to interleukin-4 receptor alpha that improves the signs and symptoms of moderate-to-severe atopic dermatitis. To determine the effects of dupilumab on Staphylococcus aureus colonization and microbial diversity on the skin, bacterial DNA was analyzed from swabs collected from lesional and nonlesional skin in a double-blind, placebo-controlled study of 54 patients with moderate-to-severe atopic dermatitis randomized (1:1) and treated with either dupilumab (200 mg weekly) or placebo for 16 weeks. Microbial diversity and relative abundance of Staphylococcus were assessed by DNA sequencing of 16S rRNA, and absolute S. aureus abundance was measured by quantitative PCR. Before treatment, lesional skin had lower microbial diversity and higher overall abundance of S. aureus than nonlesional skin. During dupilumab treatment, microbial diversity increased and the abundance of S. aureus decreased. Pronounced changes were seen in nonlesional and lesional skin. Decreased S. aureus abundance during dupilumab treatment correlated with clinical improvement of atopic dermatitis and biomarkers of type 2 immunity. We conclude that clinical improvement of atopic dermatitis that is mediated by interleukin-4 receptor alpha inhibition and the subsequent suppression of type 2 inflammation is correlated with increased microbial diversity and reduced abundance of S. aureus. identifier: NCT01979016.

RevDate: 2019-06-28

Goss-Souza D, Mendes LW, Rodrigues JLM, et al (2019)

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.

Microbial ecology pii:10.1007/s00248-019-01401-y [Epub ahead of print].

Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.

RevDate: 2019-06-28

Jeong SY, Lee CH, Yi T, et al (2019)

Effects of Quorum Quenching on Biofilm Metacommunity in a Membrane Bioreactor.

Microbial ecology pii:10.1007/s00248-019-01397-5 [Epub ahead of print].

Quorum quenching (QQ) has received attention for the control of biofilms, e.g., biofilms that cause biofouling in membrane bioreactors (MBRs). Despite the efficacy of QQ on biofouling, it is elusive how QQ influences biofilm formation on membranes. A pilot-scale QQ-MBR and non-QQ-MBR were identically operated for 4 days and 8 days to destructively sample the membranes. QQ prolonged the membrane filterability by 43% with no harmful influence on MBR performance. qPCR showed no effect of QQ on microbial density during either of these time periods. Community comparisons revealed that QQ influenced the bacterial and fungal community structures, and the fungal structure corresponded with the bacterial structure. Metacommunity and spatial analyses showed that QQ induced structural variation rather than compositional variation of bacteria and fungi. Moreover, QQ considerably enhanced the bacterial dispersal across membrane during the early development. As the dispersal enhancement by QQ counteracted the ecological drift, it eliminated the distance-decay relationship, reflecting a neutral theory archetype of metacommunity. Network analyses showed that QQ substantially reduced the amount and magnitude of interactions, e.g., competition and cooperation, for bacteria and fungi, and weakened their network structures, irrespective of time. Additionally, QQ suppressed the growth of specific microbial species (e.g., Acinetobacter), abundant and widespread at the early stage. These findings suggest that QQ influenced the community dynamics at the regional and local levels, correspondingly the ecological selection and dispersal processes, during the biofilm development.

RevDate: 2019-06-28

Lee J, Han G, Kim JW, et al (2019)

Taxon-Specific Effects of Lactobacillus on Drosophila Host Development.

Microbial ecology pii:10.1007/s00248-019-01404-9 [Epub ahead of print].

Commensal microbiota heavily influence metazoan host physiology. Drosophila melanogaster has been proven a valuable animal model for studying many aspects of host-microbiota interaction. Lactobacillus are the most common human probiotics and are also one of the major symbiotic bacteria in Drosophila. Although the beneficial effects of Lactobacillus on fly development and physiology have been recognized, how broadly these effects are observed across the Lactobacillus taxa remains largely unknown. In this study, four Lactobacillus species including five strains of L. plantarum were examined for their effects on fly larval development. Monoassociation of germ-free flies with L. rhamnosus (GG) most strongly accelerated fly larval development. Monoassociation with L. plantarum moderately accelerated fly development, but monoassociation with L. reuteri or L. sakei had marginal effects, despite similar bacterial loads in the host gut. An L. plantarum strain previously isolated from our lab rarely enhanced larval development, confirming the strain-specific effects of L. plantarum. The correlation between development-promoting effects and protein digestion activity in the host gut was found only among the members of L. plantarum species. Moreover, the cytoprotective response in the host gut known to be induced by L. plantarum was not correlated with development-promoting effects among any of the bacteria tested. Our results suggest that a broad range of Lactobacillus taxa are able to reside in the fly gut, but their ability to enhance host larval development is highly varied. This study may aid our understanding of the basic principles underlying the beneficial effects of probiotic commensal bacteria on metazoan development.

RevDate: 2019-06-28

Frau A, Kenny JG, Lenzi L, et al (2019)

DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies.

Scientific reports, 9(1):9328 pii:10.1038/s41598-019-44974-x.

Microbial ecology studies are often performed through extraction of metagenomic DNA followed by amplification and sequencing of a marker. It is known that each step may bias the results. These biases have been explored for the study of bacterial communities, but rarely for fungi. Our aim was therefore to evaluate methods for the study of the gut mycobiome. We first evaluated DNA extraction methods in fungal cultures relevant to the gut. Afterwards, to assess how these methods would behave with an actual sample, stool from a donor was spiked with cells from the same cultures. We found that different extraction kits favour some species and bias against others. In terms of amplicon sequencing, we evaluated five primer sets, two for ITS2 and one for ITS1, 18S and 28S rRNA. Results showed that 18S rRNA outperformed the other markers: it was able to amplify all the species in the mock community and to discriminate among them. ITS primers showed both amplification and sequencing biases, the latter related to the variable length of the product. We identified several biases in the characterisation of the gut mycobiome and showed how crucial it is to be aware of these before drawing conclusions from the results of these studies.

RevDate: 2019-06-28

Richardson E, JB Dacks (2019)

Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight.

Microorganisms, 7(6): pii:microorganisms7060178.

Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world's largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.

RevDate: 2019-06-27

Azarian T, Ridgway JP, Yin Z, et al (2019)

Long-Term Intrahost Evolution of Methicillin Resistant Staphylococcus aureus Among Cystic Fibrosis Patients With Respiratory Carriage.

Frontiers in genetics, 10:546.

Staphylococcus aureus is the most commonly identified airway colonizer of cystic fibrosis (CF) patients, and infections with methicillin-resistant S. aureus (MRSA) are associated with poor outcomes. Yet, little is known about the intrahost evolution of S. aureus among CF patients. We investigated convergent evolution and adaptation of MRSA among four CF patients with long-term respiratory carriage. For each patient, we performed whole-genome sequencing on an average of 21 isolates (range: 19-23) carried for a mean of 1,403 days (range: 903-1,679), including 25 pairs of isolates collected on the same day. We assessed intrahost diversity, population structure, evolutionary history, evidence of switched intergenic regions (IGRs), and signatures of adaptation in the context of patient age, antibiotic treatment, and co-colonizing microbes. Phylogenetic analysis delineated distinct multilocus sequence type ST5 (n = 3) and ST72 (n = 1) clonal populations in addition to sporadic, non-clonal isolates, and uncovered a putative transmission event. Variation in antibiotic resistance was observed within clonal populations, even among isolates collected on the same day. Rates of molecular evolution ranged from 2.21 to 8.64 nucleotide polymorphisms per year, and lineage ages were consistent with acquisition of colonization in early childhood followed by subsequent persistence of multiple sub-populations. Selection analysis of 1,622 core genes present in all four clonal populations (n = 79) found 11 genes variable in three subjects - most notably, ATP-dependent protease clpX, 2-oxoglutarate dehydrogenase odhA, fmtC, and transcription-repair coupling factor mfd. Only one gene, staphylococcal protein A (spa), was found to have evidence of gene-wide diversifying selection. We identified three instances of intrahost IGR switching events, two of which flanked genes related to quorum sensing. The complex microbial ecology of the CF airway poses challenges for management. We illustrate appreciable intrahost diversity as well as persistence of a dominant lineage. We also show that intrahost adaptation is a continual process, despite purifying selective pressure, and provide targets that should be investigated further for their function in CF adaptation.

RevDate: 2019-06-27

McNamara PJ (2019)

mSphere of Influence: Engineering Microbes.

mSphere, 4(3): pii:4/3/e00317-19.

Patrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers "Bacterial community structure in the drinking water microbiome is governed by filtration processes" (A. J. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 46:8851-8859, 2012, and "Differential resistance of drinking water bacterial populations to monochloramine disinfection" (T. Chiao, T. M. Clancy, A. Pinto, C. Xi, and L. Raskin, Environ Sci Technol 48:4038-4047, 2014, by Lutgarde Raskin and colleagues made an impact on him by providing a foundation for the study of microbial ecology in engineering drinking water treatment plants and drinking water distribution systems.

RevDate: 2019-06-26

Bayer B, Pelikan C, Bittner MJ, et al (2019)

Proteomic Response of Three Marine Ammonia-Oxidizing Archaea to Hydrogen Peroxide and Their Metabolic Interactions with a Heterotrophic Alphaproteobacterium.

mSystems, 4(4): pii:4/4/e00181-19.

Ammonia-oxidizing archaea (AOA) play an important role in the nitrogen cycle and account for a considerable fraction of the prokaryotic plankton in the ocean. Most AOA lack the hydrogen peroxide (H2O2)-detoxifying enzyme catalase, and some AOA have been shown to grow poorly under conditions of exposure to H2O2 However, differences in the degrees of H2O2 sensitivity of different AOA strains, the physiological status of AOA cells exposed to H2O2, and their molecular response to H2O2 remain poorly characterized. Further, AOA might rely on heterotrophic bacteria to detoxify H2O2, and yet the extent and variety of costs and benefits involved in these interactions remain unclear. Here, we used a proteomics approach to compare the protein profiles of three Nitrosopumilus strains grown in the presence and absence of catalase and in coculture with the heterotrophic alphaproteobacterium Oceanicaulis alexandrii We observed that most proteins detected at a higher relative abundance in H2O2-exposed Nitrosopumilus cells had no known function in oxidative stress defense. Instead, these proteins were putatively involved in the remodeling of the extracellular matrix, which we hypothesize to be a strategy limiting the influx of H2O2 into the cells. Using RNA-stable isotope probing, we confirmed that O. alexandrii cells growing in coculture with the Nitrosopumilus strains assimilated Nitrosopumilus-derived organic carbon, suggesting that AOA could recruit H2O2-detoxifying bacteria through the release of labile organic matter. Our results contribute new insights into the response of AOA to H2O2 and highlight the potential ecological importance of their interactions with heterotrophic free-living bacteria in marine environments.IMPORTANCE Ammonia-oxidizing archaea (AOA) are the most abundant chemolithoautotrophic microorganisms in the oxygenated water column of the global ocean. Although H2O2 appears to be a universal by-product of aerobic metabolism, genes encoding the hydrogen peroxide (H2O2)-detoxifying enzyme catalase are largely absent in genomes of marine AOA. Here, we provide evidence that closely related marine AOA have different degrees of sensitivity to H2O2, which may contribute to niche differentiation between these organisms. Furthermore, our results suggest that marine AOA rely on H2O2 detoxification during periods of high metabolic activity and release organic compounds, thereby potentially attracting heterotrophic prokaryotes that provide this missing function. In summary, this report provides insights into the metabolic interactions between AOA and heterotrophic bacteria in marine environments and suggests that AOA play an important role in the biogeochemical carbon cycle by making organic carbon available for heterotrophic microorganisms.

RevDate: 2019-06-26

Dimitriu T, Marchant L, Buckling A, et al (2019)

Bacteria from natural populations transfer plasmids mostly towards their kin.

Proceedings. Biological sciences, 286(1905):20191110.

Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Particularly, interactions between donor hosts and potential recipients are understudied. Here, we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in plasmid transfer. We uncover extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive two different plasmids, R1 and RP4. Overall, transfer is strongly biased towards clone-mates, but not correlated to genetic distance when donors and recipients are not clone-mates. Transfer is limited by the presence of a functional restriction-modification system in recipients, suggesting sharing of strain-specific defence systems contributes to bias towards kin. Such restriction of transfer to kin sets the stage for longer-term coevolutionary interactions leading to mutualism between plasmids and bacterial hosts in natural communities.

RevDate: 2019-06-25

Kunath BJ, Minniti G, Skaugen M, et al (2019)

Metaproteomics: Sample Preparation and Methodological Considerations.

Advances in experimental medicine and biology, 1073:187-215.

Meta-omic techniques have progressed rapidly in the past decade and are frequently used in microbial ecology to study microorganisms in their natural ecosystems independent from culture restrictions. Metaproteomics, in combination with metagenomics, enables quantitative assessment of expressed proteins and pathways from individual members of the consortium. Together, metaproteomics and metagenomics can provide a detailed understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize nutrients, and these insights can be obtained directly from environmental samples. Here, we outline key aspects of sample preparation, database generation, and other methodological considerations that are required for successful quantitative metaproteomic analyses and we describe case studies on the integration with metagenomics for enhanced functional output.

RevDate: 2019-06-25

Fiałkowska E, Fiałkowski W, A Pajdak-Stós (2019)

The Relations Between Predatory Fungus and Its Rotifer Preys as a Noteworthy Example of Intraguild Predation (IGP).

Microbial ecology pii:10.1007/s00248-019-01398-4 [Epub ahead of print].

Intraguild predation (IGP) is a widespread interaction combining predation and competition. We investigated a unique IGP example among predacious fungus Zoophagus sp. and two rotifers, the predacious Cephalodella gibba and the common prey Lecane inermis. We checked the influence of the fungus on its competitor C. gibba and their joint influence on shared prey L. inermis, and the impact of the competitive predator on the growth of predacious fungus. The experiment on grown mycelium showed that Zoophagus strongly, negatively influences the growth of C. gibba (intermediate consumer) whose number did not increase throughout the experiment. The intermediate consumer was also trapped by Zoophagus and become extinct when it was its only prey, whereas in the absence of the fungus and with unlimited access to prey, its number grew quickly. As only few C. gibba were trapped by fungi when common preys were present, competition for food seems to have stronger effect on intermediate consumer population than predation. The experiment with conidia of the fungus showed that intermediate consumer significantly limits the growth of Zoophagus by reducing the number of available prey. It was observed that although the fungus can trap C. gibba, the latter does not support its growth. Trapping the intermediate consumer might serve to eliminate a competitor rather than to find a source of food. The chances of survival for L. inermis under the pressure of the two competing predators are scarce. It is the first example of IGP involving representatives of two kingdoms: Fungi and Animalia.

RevDate: 2019-06-25

Kraemer SA, Ramachandran A, GG Perron (2019)

Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy.

Microorganisms, 7(6): pii:microorganisms7060180.

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development.

RevDate: 2019-06-24

Forger LV, Woolf MS, Simmons TL, et al (2019)

A eukaryotic community succession based method for postmortem interval (PMI) estimation of decomposing porcine remains.

Forensic science international, 302:109838 pii:S0379-0738(19)30246-4 [Epub ahead of print].

Recent, short-term studies on porcine and human models (albeit with few replicates) demonstrated that the succession of the microbial community of remains may be used to estimate time since death. Using a porcine model (N=6) over an extended period of time (1703 ADD, or two months), this study characterized the eukaryote community of decomposing remains. Skin microbial samples were collected from the torso of each set of remains every day during the first week, on alternate days during the second week, and once a week for the remainder of the 60-day period; all collection intervals were recorded in accumulated degree days (ADD). The eukaryote community of each sample was determined using 18S ribosomal DNA (rDNA) MiSeq high throughput sequencing; data were analyzed in the Mothur pipeline (v1.39.5) and in IBM SPSS and R statistical packages. The relative abundance of eukaryote taxa across ADD/Days and an Analysis of Molecular Variance (AMOVA) indicated similarities between sequential ADD/Days, but significant differences in the eukaryote communities as broad stage 'milestones' of decomposition were reached. Fresh remains (0-57 ADD/0-2 Days; exhibiting a total body score (TBS) of 0-10) were characterized by the combined presence of Saccharomycetaceae, Debaryomycetaceae, Trichosporonaceae, Rhabditida, and Trichostomatia. During bloat and active decay (87-209 ADD/3-7 Days; exhibiting TBS of 11-20), Diptera was the most abundant eukaryotic taxa. During advanced decay stage (267-448 ADD/9-15 Days; exhibiting TBS of 21-25), Rhabditida was the most dominant eukaryote. Dry/skeletal remains (734-1703 ADD/26-61 Days; TBS≥26) were dominated by fungal families Dipodascaceae, Debaryomycetaceae, Trichosporonaceae, and Sporidiobolaceae. Using the family-level eukaryote taxonomic data for the entire study, random forest modelling explained 89.58% of the variation in ADD/Days, with a root mean square error (RMSE) of 177.55 ADD (≈6 days). Overall, these results highlight the importance of the microbial eukaryote community during the process of decomposition and in estimation of PMI.

RevDate: 2019-06-24

Zealand AM, Mei R, Roskilly AP, et al (2019)

Molecular microbial ecology of stable versus failing rice straw anaerobic digesters.

Microbial biotechnology [Epub ahead of print].

Waste rice straw (RS) is generated in massive quantities around the world and is often burned, creating greenhouse gas and air quality problems. Anaerobic digestion (AD) may be a better option for RS management, but RS is presumed to be comparatively refractory under anaerobic conditions without pre-treatment or co-substrates. However, this presumption assumes frequent reactor feeding regimes but less frequent feeding may be better for RS due to slow hydrolysis rates. Here, we assess how feeding frequency (FF) and organic loading rate (OLR) impacts microbial communities and biogas production in RS AD reactors. Using 16S rDNA amplicon sequencing and bioinformatics, microbial communities from five bench-scale bioreactors were characterized. At low OLR (1.0 g VS l-1 day-1), infrequently fed units (once every 21 days) had higher specific biogas yields than more frequent feeding (five in 7 days), although microbial community diversities were statistically similar (P > 0.05; ANOVA with Tukey comparison). In contrast, an increase in OLR to 2.0 g VS l-1 day-1 significantly changed Archaeal and fermenting Eubacterial sub-communities and the least frequency fed reactors failed. 'Stable' reactors were dominated by Methanobacterium, Methanosarcina and diverse Bacteroidetes, whereas 'failed' reactors saw shifts towards Clostridia and Christensenellaceae among fermenters and reduced methanogen abundances. Overall, OLR impacted RS AD microbial communities more than FF. However, combining infrequent feeding and lower OLRs may be better for RS AD because of higher specific yields.

RevDate: 2019-06-24

Zhong X, Xu G, Min GS, et al (2019)

Can tidal events influence monitoring surveys using periphytic ciliates based on biological trait analysis in marine ecosystems?.

Marine pollution bulletin, 142:452-456.

To identify the influence of tidal events on community functioning of periphytic ciliates for monitoring program and community research using biological trait analysis, a 3-month baseline survey was conducted in Korean coastal waters using the polyurethane foam enveloped slide system (PFES) and conventional slide system (CS). Although the periphytic ciliate communities had similar biological trait categories, they represented considerable differences in community functioning and functional diversity measures within the PFES and CS systems. Multivariate analyses revealed different ways of the temporal shift in community functioning of the ciliates in both systems. The dispersion analysis demonstrated that the CS system was sensitive to the strong disturbance of tidal current and circulation compared to the PFES system. These findings suggest that the strong tidal event may significantly influence the output of analysis on community functioning of periphytic ciliates for bioassessment in marine ecosystems.

RevDate: 2019-06-23

Souza FFC, Rissi DV, Pedrosa FO, et al (2019)

Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest.

The Science of the total environment, 688:83-86 pii:S0048-9697(19)32791-3 [Epub ahead of print].

Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.

RevDate: 2019-06-23

Boyle MA, Kearney A, Carling P, et al (2019)

'Off the Rails': Hospital bed rail design, contamination, and the evaluation of their microbial ecology.

The Journal of hospital infection pii:S0195-6701(19)30266-X [Epub ahead of print].

Microbial contamination of the near-patient environment is an acknowledged reservoir for nosocomial pathogens. The hospital bed and specifically bed rails have been shown to be frequently and heavily contaminated in observational and interventional studies. While the complexity of bedrail design has evolved over the years, the microbial contamination of these surfaces has been incompletely evaluated. In many published studies, key design variables are not described, compromising the extrapolation of results to other settings. This report reviews the evolving structure of hospital beds and bed rails, the possible impact of different design elements on microbial contamination and their role in pathogen transmission. Our findings support the need for clearly defined standardized assessment protocols to accurately assess bedrail and similar patient zone surfaces levels of contamination, as part of environmental hygiene investigations.

RevDate: 2019-06-22

Jung MY, Gwak JH, Rohe L, et al (2019)

Indications for enzymatic denitrification to N2O at low pH in an ammonia-oxidizing archaeon.

The ISME journal pii:10.1038/s41396-019-0460-6 [Epub ahead of print].

Nitrous oxide (N2O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N2O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N2O by pure cultures of two ammonia-oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an ammonia-oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N2O. However, changes of 15N site preference (SP) values within the N2O molecule (as indicators of pathways for N2O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, 15N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N2O in all strains, but the incorporation rate was different for each ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N2O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N2O at low pH.

RevDate: 2019-06-22

Webster TM, N Fierer (2019)

Microbial dynamics of biosand filters and contributions of the microbial food web to effective treatment of wastewater-impacted water sources.

Applied and environmental microbiology pii:AEM.01142-19 [Epub ahead of print].

Biosand filtration systems are widely used for drinking water treatment, from household-level, intermittently-operated filters to large-scale continuous municipal systems. While it is well-established that microbial activity within the filter is essential for the removal of potential pathogens and other contaminants, the microbial ecology of these systems and how microbial succession relates to their performance remain poorly resolved. We determined how different source waters influence the composition, temporal dynamics, and performance of microbial communities in intermittently-operated biosand filters. We operated lab-scale biosand filters, adding daily inputs from two contrasting water sources with differing nutrient concentrations, and found that total coliform removal increased and became less variable after four weeks, regardless of water source. Total effluent biomass was also lower than influent for both water sources. Bacterial community composition, assessed via cultivation-independent DNA sequencing, varied by water source, sample type (influent, effluent, or sand), and time. Despite these differences, we identified specific taxa that were consistently removed, including common aquatic and wastewater bacteria. In contrast, taxa consistently more abundant in the sand and effluent included predatory, intracellular, and symbiotic bacteria.IMPORTANCEAlthough microbial activities are known to contribute to the effectiveness of biosand filtration for drinking water treatment, we have a limited understanding of what microbial groups are most effectively removed, colonize the sand, or make it through the filter. This study tracked the microbial communities in the influent, sand, and effluent of lab-scale, intermittently-operated biosand filters over 8 weeks. These results represent the most detailed and time-resolved investigation of the microbial communities in biosand filters typical of those implemented at the household level in many developing countries. We show the importance of the microbial food web in biosand filtration and we identified taxa that are preferentially removed from wastewater-impacted water sources. We found consistent patterns in filter effectiveness from source waters with differing nutrient loads and, likewise, identified specific bacterial taxa that were consistently more abundant in effluent waters, taxa that are important targets for further study and post-treatment.

RevDate: 2019-06-21

Wang S, Zheng X, Xia H, et al (2019)

Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing.

PloS one, 14(6):e0218611 pii:PONE-D-19-09143.

The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.

RevDate: 2019-06-21

Brehony C, McGrath E, Brennan W, et al (2019)

An MLST approach to support tracking of plasmids carrying OXA-48-like carbapenemase.

The Journal of antimicrobial chemotherapy, 74(7):1856-1862.

OBJECTIVES: The prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Enterobacteriaceae Reference Laboratory Service for a 13 month period (2016-17).

METHODS: A total of 109 OXA-48-producing non-duplicate clinical isolates from 16 submitting centres were sequenced. Using a gene-by-gene approach, isolate genomes were characterized by MLST and core genome MLST, and the presence of antimicrobial resistance determinants was determined. Reference mapping and a novel plasmid MLST-type approach was applied to determine plasmid background.

RESULTS: The OXA-48-like-producing isolates were Escherichia coli (n = 56), Klebsiella spp. (n = 46) and Enterobacter cloacae (n = 7). Amongst the E. coli isolates there were 37 different STs and amongst the Klebsiella spp. isolates there were 27 different STs. blaOXA-48 was present in 105/109 (96.3%) of isolates. Based on mapping analysis and detection of the pOXA-48 IncL-type plasmid replicon and backbone genes, a pOXA-48-like plasmid was identified in 93/109 isolates (85.3%). The remaining isolates (n = 16; 14.7%) harboured blaOXA-48-like genes in unknown environments. Using a gene-by-gene approach two pOXA-48-like plasmid groups with 2/71 pOXA-48-like locus differences between them were identified.

CONCLUSIONS: In Ireland we found a diversity of genotypes associated with OXA-48-like-producing clinical isolates with the IncL pOXA-48 plasmid type predominating as the blaOXA-48 genetic environment. A plasmid MLST approach can rapidly identify plasmids associated with outbreaks and monitor spread of types temporally and geographically.

RevDate: 2019-06-21

Otieno D, Pei Y, Gu I, et al (2019)

Effect of Quercetin on Non-shivering Thermogenesis and Intestinal Microbial Populations (P06-037-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz031.P06-037-19.

Objectives: Activation of non-shivering thermogenesis in adipose tissues and alteration in intestinal microbiome have been linked with improved obese condition. With emerging evidences of dietary compounds to prevent obesity, the objective of this study was to examine whether quercetin activates non-shivering thermogenesis in adipose tissues and influences intestinal microbiome, which eventually improves obese condition.

Methods: Four-week-old C57BL/6 male mice were fed either a low-fat diet (LFD) or a high-fat diet (HFD) with or without 1% quercetin (Q) for 16 weeks. On the completion of the feeding study, brown adipose tissue (BAT), white adipose tissue (WAT), and cecum were collected. Total RNA was extracted from BAT and WAT, and then cDNA was synthesized. The expression of genes that are involved in the regulation of non-shivering thermogenesis such as uncoupling protein 1 (ucp1), cell death-inducing DFFA-like effector A (cidea), peroxisome proliferator-activated receptor gamma (pparγ), pparγ-coactivator 1 alpha (pgc1α), fibroblast growth factor 21 (fgf21), positive regulatory domain containing 16 (prdm16), and T-box protein 1 (tbx1) were determined by a real-time PCR. The expression of the proteins such as UCP1 and AMP-activated protein kinase (AMPK) was assessed by western blot analysis. Microbial populations in cecum were analyzed via the Illumnia MiSeq sequencing platform and QIIME (Quantitative Insights Into Microbial Ecology) Software.

Results: Mice fed HFDQ showed reduced body weight and retroperitoneal (R) WAT weight compared to mice fed HFD. Quercetin supplementation increased the expression of ucp1, prdm16, pgc1α, cidea, and tbx1 genes in BAT and RWAT of mice fed HFD. The expression of UCP1 protein and phosphorylation of AMPK were increased. However, browning effect was not observed in other WATs. Mice fed LFDQ and HFDQ exhibited higher relative abundance of Bacteroidetes than mice fed LFD and HFD whereas the relative abundance of Firmicutes was decreased.

Conclusions: Quercetin may be a potential dietary compound that increases energy metabolism by activating BAT and attracting beige adipocytes in RWAT. In addition, quercetin-induced energy metabolism may have a correlation with changes of microbial populations in intestine.

Funding Sources: The work was supported by USDA.

RevDate: 2019-06-21

Hammerbacher A, Coutinho TA, J Gershenzon (2019)

Roles of plant volatiles in defense against microbial pathogens and microbial exploitation of volatiles.

Plant, cell & environment [Epub ahead of print].

Plants emit a large variety of volatile organic compounds during infection by pathogenic microbes, including terpenes, aromatics, nitrogen-containing compounds, fatty acid derivatives, as well as the volatile plant hormones, methyl jasmonate and methyl salicylate. Given the general anti-microbial activity of plant volatiles and the timing of emission following infection, these compounds have often been assumed to function in defense against pathogens without much solid evidence. In this review we critically evaluate current knowledge on the toxicity of volatiles to fungi, bacteria and viruses and their role in plant resistance as well as how they act to induce systemic resistance in uninfected parts of the plant and in neighboring plants. We also discuss how microbes can detoxify plant volatiles and exploit them as nutrients, attractants for insect vectors, and inducers of volatile emissions that stimulate immune responses that make plants more susceptible to infection. Although much more is known on plant volatile-herbivore interactions, knowledge of volatile-microbe interactions is growing and it may eventually be possible to harness plant volatiles to reduce disease in agriculture and forestry. Future research in this field can be facilitated by making use of the analytical and molecular tools generated by the prolific research on plant-herbivore interactions.

RevDate: 2019-06-20

Trifi H, Najjari A, Achouak W, et al (2019)

Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.

Genomics pii:S0888-7543(19)30022-9 [Epub ahead of print].

Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria recoverable into (1) removal of radioactive elements and toxic heavy metals (2) promotion of plant growth (3) oxidation and (4) reduction of sulfate.

RevDate: 2019-06-20

Myer PR (2019)

Bovine Genome-Microbiome Interactions: Metagenomic Frontier for the Selection of Efficient Productivity in Cattle Systems.

mSystems, 4(3): pii:4/3/e00103-19.

The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. Because these microbial communities are critical for host nutrient utilization and contribute to the metabolic capacity of the rumen, past research has aimed to define host-microbe symbioses in cattle by examining the rumen and lower gut microbiomes with respect to production phenotypes, such as feed efficiency. However, as the field of bovine gut microbial ecology progresses, multidisciplinary approaches must be employed, combining host genomics and other omics-based techniques to understand the complex host-microbe network. In this perspective, I discuss the direction of the field of bovine gut microbial ecology with regard to feed efficiency and explore how the grand challenge of such research will be to maintain host-efficient gut microbiomes in cattle production through manipulations of genome-microbiome interactions.

RevDate: 2019-06-20

Tedersoo L, S Anslan (2019)

Towards PacBio-based pan-eukaryote metabarcoding using full-length ITS sequences.

Environmental microbiology reports [Epub ahead of print].

Development of high-throughput sequencing techniques have greatly benefited our understanding about microbial ecology; yet the methods producing short reads suffer from species-level resolution and uncertainty of identification. Here we optimize PacBio-based metabarcoding protocols covering the Internal Transcribed Spacer (ITS region) and partial Small Subunit (SSU) of the rRNA gene for species-level identification of all eukaryotes, with a specific focus on Fungi (including Glomeromycota) and Stramenopila (particularly Oomycota). Based on tests on composite soil samples and mock communities, we propose best suitable degenerate primers, ITS9munngs + ITS4ngsUni for eukaryotes and selected groups therein and discuss pros and cons of long read-based identification of eukaryotes. This article is protected by copyright. All rights reserved.

RevDate: 2019-06-20

Della Mónica IF, Godeas AM, JM Scervino (2019)

In Vivo Modulation of Arbuscular Mycorrhizal Symbiosis and Soil Quality by Fungal P Solubilizers.

Microbial ecology pii:10.1007/s00248-019-01396-6 [Epub ahead of print].

Phosphorus (P) is an essential nutrient with low bioavailability in soils for plant growth. The use of P solubilization fungi (PSF) has arisen as an eco-friendly strategy to increase this nutrient's bioavailability. The effect of PSF inoculation and its combination with P-transporting organisms (arbuscular mycorrhizal fungi, AMF) on plant growth has been previously studied. However, these studies did not evaluate the combined effect of PSF and AMF inoculation on plant growth, symbiosis, and soil quality. Therefore, the aim of this study is to assess the impact of PSF on the AMF-wheat symbiosis establishment and efficiency, considering the effect on plant growth and soil quality. We performed a greenhouse experiment with wheat under different treatments (+/-AMF: Rhizophagus irregularis; +/-PSF strains: Talaromyces flavus, T. helicus L7B, T. helicus N24, and T. diversus) and measured plant growth, AMF root colonization, symbiotic efficiency, and soil quality indicators. No interaction between PSF and R. irregularis was found in wheat growth, showcasing that their combination is not better than single inoculation. T. helicus strains did not interfere with the AMF-wheat symbiosis establishment, while T. diversus and T. flavus decreased it. The symbiotic efficiency was increased by T. flavus and T. helicus N24, and unchanged with T. helicus L7B and T. diversus inoculation. The soil quality indicators were higher with microbial co-inoculation, particularly the alkaline phosphatases parameter, showing the beneficial role of fungi in soil. This work highlights the importance of microbial interactions in the rhizosphere for crop sustainability and soil quality improvement, assessing the effects of PSF on AMF-wheat symbiosis.

RevDate: 2019-06-20

Fan Z, Lu S, Liu S, et al (2019)

Changes in Plant Rhizosphere Microbial Communities under Different Vegetation Restoration Patterns in Karst and Non-karst Ecosystems.

Scientific reports, 9(1):8761 pii:10.1038/s41598-019-44985-8.

Understanding how patterns of recovery and geological conditions affect microbial communities is important for determining the stability of karst ecosystems. Here, we investigated the diversity and composition of microorganisms in karst and non-karst environments under natural restoration and artificial rehabilitation conditions. The results showed no significant differences in soil microbial diversity, but the microbial communities associated with geological conditions and tree species differed significantly. Variation partitioning analysis (VPA) showed that a total of 77.3% of the variation in bacteria and a total of 69.3% of the variation in fungi could be explained by vegetation type and geological background. There were significant differences in six bacterial classes (Actinobacteria, Alphaproteobacteria, Ktedonobacteria, TK10, Gammaproteobacteria, and Anaerolineae) and nine fungal classes (Eurotiomycetes, Agaricomycetes, unclassified _p_Ascomycota, Sordariomycetes, Tremellomycetes, norank_k_Fungi, Pezizomycetes, Leotiomycetes and Archaeorhizomycetes) among the soils collected from six plots. A Spearman correlation heatmap showed that the microbial community was affected by the major soil properties. Principal coordinates analysis indicated that the microbial community of Pinus yunnanensis in the artificial forest, which was established for the protection of the environment was most similar to that in the natural secondary forest in the karst ecosystem. These findings further our understanding of microbial responses to vegetation restoration and geological conditions.

RevDate: 2019-06-19

Hounmanou YMG, Mdegela RH, Dougnon TV, et al (2019)

Tilapia (Oreochromis niloticus) as a Putative Reservoir Host for Survival and Transmission of Vibrio cholerae O1 Biotype El Tor in the Aquatic Environment.

Frontiers in microbiology, 10:1215.

Studies have reported the occurrence of Vibrio cholerae in fish but little is known about the interaction between fish and toxigenic V. cholerae as opposed to phytoplankton, which are well-established aquatic reservoirs for V. cholerae. The present study determined the role of tilapia (Oreochromis niloticus) as a reservoir host for survival and transmission of V. cholerae in aquatic environments. Three experiments were performed with one repetition each, where O. niloticus (∼2 g) kept in beakers were inoculated with four V. cholerae strains (5 × 107 cfu/mL). Firstly, infected tilapia were kept in stagnant water and fed live brine shrimp (Artemia salina) larvae daily. Secondly, infected tilapia were kept without feeding and water was changed every 24 h. Thirdly, infected tilapia were fed and water was renewed daily. Infected tilapia and non-infected controls were sacrificed on days 1, 2, 3, 7, and 14 post-inoculation and V. cholerae were enumerated in intestinal content and water. Another experiment assessed the transmission of V. cholerae from infected to non-infected tilapia. The study revealed that El Tor biotype V. cholerae O1 and V. cholerae non-O1 colonized tilapia intestines and persisted at stable concentrations during the second week of the experiment whereas the Classical biotype was undetectable after 1 week. In stagnant water with feeding, V. cholerae counts dropped to 105 cfu/ml in water and from 107 to 104 cfu/intestine in fish after 14 days. When water was renewed, counts in water decreased from 107 to 103 cfu/ml and intestinal counts went from 106 to 102 cfu/intestine regardless of feeding. All strains were transmitted from infected to naïve fish after 24 h of cohabitation. Tilapia like other fish may play an essential role in the survival and dissemination of V. cholerae O1 in aquatic environments, e.g., the seventh pandemic strains mostly. In this study, tilapia were exposed to high concentrations of V. cholerae to ensure initial uptake and follow-up studies with lower doses resembling natural concentrations of V. cholerae in the aquatic environment are needed to confirm our findings.

RevDate: 2019-06-19

El Hage R, Hernandez-Sanabria E, Calatayud Arroyo M, et al (2019)

Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem.

Frontiers in microbiology, 10:1206.

Metabolic syndrome is a growing public health concern. Efforts at searching for links with the gut microbiome have revealed that propionate is a major fermentation product in the gut with several health benefits toward energy homeostasis. For instance, propionate stimulates satiety-inducing hormones, leading to lower energy intake and reducing weight gain and associated risk factors. In (disease) scenarios where microbial dysbiosis is apparent, gut microbial production of propionate may be decreased. Here, we investigated the effect of a propionogenic bacterial consortium composed of Lactobacillusplantarum, Bacteroidesthetaiotaomicron, Ruminococcusobeum, Coprococcuscatus, Bacteroidesvulgatus, Akkermansiamuciniphila, and Veillonellaparvula for its potential to restore in vitro propionate concentrations upon antibiotic-induced microbial dysbiosis. Using the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME), we challenged the simulated colon microbiome with clindamycin. Addition of the propionogenic consortium resulted in successful colonization and subsequent restoration of propionate levels, while a positive effect on the mitochondrial membrane potential (ΔΨm) was observed in comparison with the controls. Our results support the development and application of next generation probiotics, which are composed of multiple bacterial strains with diverse functionality and phylogenetic background.

RevDate: 2019-06-19

Dai D, Wang T, Wu S, et al (2019)

Metabolic Dependencies Underlie Interaction Patterns of Gut Microbiota During Enteropathogenesis.

Frontiers in microbiology, 10:1205.

In recent decades, increasing evidence has strongly suggested that gut microbiota play an important role in many intestinal diseases including inflammatory bowel disease (IBD) and colorectal cancer (CRC). The composition of gut microbiota is thought to be largely shaped by interspecies competition for available resources and also by cooperative interactions. However, to what extent the changes could be attributed to external factors such as diet of choice and internal factors including mutual relationships among gut microbiota, respectively, are yet to be elucidated. Due to the advances of high-throughput sequencing technologies, flood of (meta)-genome sequence information and high-throughput biological data are available for gut microbiota and their association with intestinal diseases, making it easier to gain understanding of microbial physiology at the systems level. In addition, the newly developed genome-scale metabolic models that cover significant proportion of known gut microbes enable researchers to analyze and simulate the system-level metabolic response in response to different stimuli in the gut, providing deeper biological insights. Using metabolic interaction network based on pair-wise metabolic dependencies, we found the same interaction pattern in two IBD datasets and one CRC datasets. We report here for the first time that the growth of significantly enriched bacteria in IBD and CRC patients could be boosted by other bacteria including other significantly increased ones. Conversely, the growth of probiotics could be strongly inhibited from other species, including other probiotics. Therefore, it is very important to take the mutual interaction of probiotics into consideration when developing probiotics or "microbial based therapies." Together, our metabolic interaction network analysis can predict majority of the changes in terms of the changed directions in the gut microbiota during enteropathogenesis. Our results thus revealed unappreciated interaction patterns between species could underlie alterations in gut microbiota during enteropathogenesis, and between probiotics and other microbes. Our methods provided a new framework for studying interactions in gut microbiome and their roles in health and disease.

RevDate: 2019-06-19

You YA, Yoo JY, Kwon EJ, et al (2019)

Blood Microbial Communities During Pregnancy Are Associated With Preterm Birth.

Frontiers in microbiology, 10:1122.

Microbial infection of the placenta, amniotic fluid, vaginal canal, and oral cavity is known to significantly contribute to preterm birth (PTB). Although microbes can be translocated into the blood, little is known regarding the blood microbiota during pregnancy. To assess changes in the microbiome during pregnancy, blood samples were obtained 2 or 3 times during pregnancy from a cohort of 45 pregnant women enrolled between 2008 and 2010. To analyze the association with PTB, we conducted a case-control study involving 41 pregnant women upon admission for preterm labor and rupture of membrane (20 with term delivery; 21 with PTB). Bacterial diversity was assessed in number and composition between the first, second, and third trimesters in term delivered women according to 16S rRNA gene amplicon sequencing, and data were analyzed using Quantitative Insight Into Microbial Ecology (QIIME). Taxonomy was assigned using the GreenGenes 8.15.13 database. Dominant microorganisms at the phylum level in all pregnant women were identified as Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. However, the number and composition of bacteria in women with PTB differed from that in women with term delivery. Firmicutes and Bacteroidetes were more abundant in women with PTB than in women with term delivery, while Proteobacteria was less prevalent in women with PTB. At the genus level, Bacteroides, Lactobacillus, Sphingomonas, Fastidiosipila, Weissella, and Butyricicoccus were enriched in PTB samples. These observational results suggest that several taxa in the maternal blood microbiome are associated with PTB. Further studies are needed to confirm the composition of the blood microbiota in women with PTB. Additionally, the mechanism by which pathogenic microbes in maternal blood cause infection and PTB requires further analysis.

RevDate: 2019-06-17

Czechowska K, Lannigan J, Wang L, et al (2019)

Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops.

Cytometry. Part A : the journal of the International Society for Analytical Cytology, 95(6):598-644.

RevDate: 2019-06-17

Yao R, Xu L, Lu G, et al (2019)

Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation.

Evolutionary bioinformatics online, 15:1176934319848438 pii:10.1177_1176934319848438.

The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David's deer (Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.

RevDate: 2019-06-17

Tian H, Hui M, Pan P, et al (2019)

Performance and microbial ecology of biofilms adhering on aerated membrane with distinctive conditions for the treatment of domestic sewage.

Environmental technology [Epub ahead of print].

When used to treat domestic wastewater, biofilms adhering to oxygen-permeable membranes are generally altered by environmental conditions. In this study, the effect of common conditions, including salinity, temperature, air-supplying pressure, flow velocity, influent COD, and NH4-N on the biofilm structure were determined. Principal component analysis revealed that archaeal community was more easily affected by the changing conditions than bacteria. The subsequent redundancy analysis showed that salinity had the most influence on bacteria, followed by temperature, influent COD, flow velocity, pressure, and influent NH4-N. In archaea, temperature had the highest effect, followed by flow velocity, salinity, influent NH4-N, pressure, and influent COD. The key bacterial class Anaerolineae was not easily influenced by the above conditions, but the population probably contributed to the nitrogen removal. Gammaproteobacteria was promoted significantly by influent NH4-N concentration, salinity, and pressure. Betaproteobacteria and Deltaproteobacteria were apparently inhibited by the high salinity and contributed to the organic compound degradation. Flow velocity primarily promoted the growth of Alphaproteobacteria. Candidatus Nitrososphaera had a higher tolerance for salinity but lower tolerance for influent NH4-N than Nitrosomonas. The former probably played a more crucial role in ammoxidation. Methanomethylovorans might disrupt nitrogen removal because it could consume the carbon source for denitrification.

RevDate: 2019-06-16

Wedel C, Wenning M, Dettling A, et al (2019)

Resistance of thermophilic spore formers isolated from milk and whey products towards cleaning-in-place conditions: Influence of pH, temperature and milk residues.

Food microbiology, 83:150-158.

The occurrence of thermophilic spore formers in dairy powders is a major concern for producers worldwide. This study aims to investigate the resistance of thermophilic endospores towards cleaning solutions typically used for cleaning-in-place in dairy manufacturing plants. From eleven tested strains, all were able to survive an alkaline treatment (NaOH) at 65 °C for 10 min (0.5%), whereas at concentrations of 2% eight strains withstood the treatment. Acid solutions were more sporicidal. At 0.5% of HNO3, only three strains survived the treatment. Milk impurities reduced the inactivation effect of the NaOH solutions towards thermophilic spore formers. For two selected strains, a detailed kinetic inactivation in NaOH and HNO3 solutions at different temperatures was performed and non-log-linear inactivation curves were observed. This study highlights the risk of reusing cleaning solutions in dairies.

RevDate: 2019-06-16

Soverini M, Turroni S, Biagi E, et al (2019)

HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.

BMC genomics, 20(1):496 pii:10.1186/s12864-019-5883-y.

BACKGROUND: Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.

RESULTS: HumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.

CONCLUSIONS: Although blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.

RevDate: 2019-06-15

Moisan K, Cordovez V, van de Zande EM, et al (2019)

Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects.

Oecologia pii:10.1007/s00442-019-04433-w [Epub ahead of print].

Plants are ubiquitously exposed to a wide diversity of (micro)organisms, including mutualists and antagonists. Prior to direct contact, plants can perceive microbial organic and inorganic volatile compounds (hereafter: volatiles) from a distance that, in turn, may affect plant development and resistance. To date, however, the specificity of plant responses to volatiles emitted by pathogenic and non-pathogenic fungi and the ecological consequences of such responses remain largely elusive. We investigated whether Arabidopsis thaliana plants can differentiate between volatiles of pathogenic and non-pathogenic soil-borne fungi. We profiled volatile organic compounds (VOCs) and measured CO2 emission of 11 fungi. We assessed the main effects of fungal volatiles on plant development and insect resistance. Despite distinct differences in VOC profiles between the pathogenic and non-pathogenic fungi, plants did not discriminate, based on plant phenotypic responses, between pathogenic and non-pathogenic fungi. Overall, plant growth was promoted and flowering was accelerated upon exposure to fungal volatiles, irrespectively of fungal CO2 emission levels. In addition, plants became significantly more susceptible to a generalist insect leaf-chewing herbivore upon exposure to the volatiles of some of the fungi, demonstrating that a prior fungal volatile exposure can negatively affect plant resistance. These data indicate that plant development and resistance can be modulated in response to exposure to fungal volatiles.

RevDate: 2019-06-15

Szafrański SP, Kilian M, Yang I, et al (2019)

Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches.

The ISME journal pii:10.1038/s41396-019-0450-8 [Epub ahead of print].

Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and "Haemophilus ducreyi". Co-infections occurred more often in "H. ducreyi". Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine-cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.

RevDate: 2019-06-14

Giraffa G, Carminati D, E Neviani (1997)

Enterococci Isolated from Dairy Products: A Review of Risks and Potential Technological Use.

Journal of food protection, 60(6):732-738.

Enterococci are ubiquitous bacteria which frequently occur in large numbers in dairy and other food products. Although they share a number of biotechnological traits (e.g., bacteriocin production, probiotic characteristics, usefulness in dairy technology), there is no consensus on whether enterococci pose a threat as foodborne pathogens, The potential pathogenicity of lactic acid bacteria (LAB), including enterococci, in human clinical infections and their association with endocarditis have recently become a matter of controversy, in spite of the fact that foods containing enterococci have a long history of safe use. This article provides literature data available on microbial ecology, biochemical properties, production of anti- Listeria bacteriocins, and potential pathogenic traits of enterococci isolated from different dairy products.

RevDate: 2019-06-14

Hirano H, K Takemoto (2019)

Difficulty in inferring microbial community structure based on co-occurrence network approaches.

BMC bioinformatics, 20(1):329 pii:10.1186/s12859-019-2915-1.

BACKGROUND: Co-occurrence networks-ecological associations between sampled populations of microbial communities inferred from taxonomic composition data obtained from high-throughput sequencing techniques-are widely used in microbial ecology. Several co-occurrence network methods have been proposed. Co-occurrence network methods only infer ecological associations and are often used to discuss species interactions. However, validity of this application of co-occurrence network methods is currently debated. In particular, they simply evaluate using parametric statistical models, even though microbial compositions are determined through population dynamics.

RESULTS: We comprehensively evaluated the validity of common methods for inferring microbial ecological networks through realistic simulations. We evaluated how correctly nine widely used methods describe interaction patterns in ecological communities. Contrary to previous studies, the performance of the co-occurrence network methods on compositional data was almost equal to or less than that of classical methods (e.g., Pearson's correlation). The methods described the interaction patterns in dense and/or heterogeneous networks rather inadequately. Co-occurrence network performance also depended upon interaction types; specifically, the interaction patterns in competitive communities were relatively accurately predicted while those in predator-prey (parasitic) communities were relatively inadequately predicted.

CONCLUSIONS: Our findings indicated that co-occurrence network approaches may be insufficient in interpreting species interactions in microbiome studies. However, the results do not diminish the importance of these approaches. Rather, they highlight the need for further careful evaluation of the validity of these much-used methods and the development of more suitable methods for inferring microbial ecological networks.

RevDate: 2019-06-13

Johnson AJ, Vangay P, Al-Ghalith GA, et al (2019)

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.

Cell host & microbe, 25(6):789-802.e5.

Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: NCT03610477.

RevDate: 2019-06-13

Ali M, Wang Z, Salam KW, et al (2019)

Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant.

Environmental science & technology [Epub ahead of print].

In aerobic granular sludge (AGS) systems, different-sized microbial aggregates having different solids retention time (SRT) coexist in the same reactor compartment and are subjected to the same influent wastewater. Thus, the AGS system provides a unique ecosystem to study the importance of local (species sorting) and regional (immigration) processes in bacterial community assembly. The microbial communities of different-sized aggregates (flocs <0.2 mm, small granules (0.2-1.0 mm) and large granules >1.0 mm), influent wastewater, excess sludge and effluent of a full-scale AGS plant were characterized over a steady-state operation period of 6 months. Amplicon sequencing was integrated with mass balance to determine the SRT and net growth rate of operational taxonomic units (OTUs). We found strong evidence of species sorting as opposed to immigration, which was significantly higher at short SRT (i.e., flocs and small granules) than that at long SRT (large granules). Rare OTUs in wastewater belonging to putative functional groups responsible for nitrogen and phosphorus removal were progressively enriched with an increase in microbial aggregates size. In contrast, fecal- and sewage infrastructure-derived microbes progressively decreased in relative abundance with increase in microbial aggregate size. These findings highlight the importance of AGS as a unique model ecosystem to study fundamental microbial ecology concepts.

RevDate: 2019-06-13

Zhang B, Xu S, Xu W, et al (2019)

Leveraging Fecal Bacterial Survey Data to Predict Colorectal Tumors.

Frontiers in genetics, 10:447.

Colorectal cancer (CRC) ranks second in cancer-associated mortality and third in the incidence worldwide. Most of CRC follow adenoma-carcinoma sequence, and have more than 90% chance of survival if diagnosed at early stage. But the recommended screening by colonoscopy is invasive, expensive, and poorly adhered to. Recently, several studies reported that the fecal bacteria might provide non-invasive biomarkers for CRC and precancerous tumors. Therefore, we collected and uniformly re-analyzed these published fecal 16S rDNA sequencing datasets to verify the association and identify biomarkers to classify and predict colorectal tumors by random forest method. A total of 1674 samples (330 CRC, 357 advanced adenoma, 141 adenoma, and 846 control) from 7 studies were analyzed in this study. By random effects model and fixed effects model, we observed significant differences in alpha-diversity and beta-diversity between individuals with CRC and the normal colon, but not between adenoma and the normal. We identified various bacterial genera with significant odds ratios for colorectal tumors at different stages. Through building random forest model with 10-fold cross-validation as well as new test datasets, we classified individuals with CRC, advanced adenoma, adenoma and normal colon. All approaches obtained comparable performance at entire OTU level, entire genus level, and the common genus level as measured using AUC. When combined all samples, the AUC of random forest model based on 12 common genera reached 0.846 for CRC, although the predication performed poorly for advance adenoma and adenoma.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
21454 NE 143rd Street
Woodinville, WA 98077

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )