Showing papers in "Fems Microbiology Letters in 2020"

Microbial sources of polyunsaturated fatty acids (PUFAs) and the prospect of organic residues and wastes as growth media for PUFA-producing microorganisms

Abstract: The discovery of non-fish sources of polyunsaturated fatty acids (PUFAs) is of great biotechnological importance. Although various oleaginous microalgae and fungi are able of accumulating storage lipids (single cell oils - SCOs) containing PUFAs, the industrial applications utilizing these organisms are rather limited due to the high-fermentation cost. However, combining SCO production with other biotechnological applications, including waste and by-product valorization, can overcome this difficulty. In the current review, we present the major sources of fungi (i.e. members of Mucoromycota, fungoid-like Thraustochytrids and genetically modified strains of Yarrowia lipolytica) and microalgae (e.g. Isochrysis, NannochloropsisandTetraselmis) that have come recently to the forefront due to their ability to produce PUFAs. Approaches adopted in order to increase PUFA productivity and the potential of using various residues, such as agro-industrial, food and aquaculture wastes as fermentation substrates for SCO production have been considered and discussed. We concluded that several organic residues can be utilized as feedstock in the SCO production increasing the competitiveness of oleaginous organisms against conventional PUFA producers.

Intestinal fermentation in vitro models to study food-induced gut microbiota shift: an updated review.

Abstract: In vitro gut fermentation models were firstly introduced in nutrition and applied microbiology research back in the 1990s. These models have improved greatly during time, mainly over the resemblance to the complexity of digestion stages, the replication of experimental conditions, the multitude of ecological parameters to assay. The state of the science is that the most competitive models shall include a complex gut microbiota, small working volumes, distinct interconnected compartments and rigorous bio-chemical and ecological settings, controlled by a computer, as well as a free-hands accessibility, not to contaminate the mock microbiota. These models are a useful tool to study the impact of a given diet compound, e.g. prebiotics, on the human gut microbiota. The principal application is to focus on the shift of the core microbial groups and selected species together with their metabolites, assaying their diversity, richness and abundance in the community over time. Besides, it is possible to study how a compound is digested, which metabolic pathways are triggered, and the type and quantity of microbial metabolites produced. Further prospective should focus on challenges with pathogens as well as on ecology of gut syndromes. In this minireview an updated presentation of the most used intestinal models is presented, basing on their concept, technical features, as well as on research applications.

The hydrogen threshold of obligately methyl-reducing methanogens

Abstract: Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.

3D biofilms: in search of the polysaccharides holding together lichen symbioses.

Abstract: Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes.

Production of added-value microbial metabolites during growth of yeast strains on media composed of biodiesel-derived crude glycerol and glycerol/xylose blends.

Abstract: A total of 11 yeast strains of Yarrowia lipolytica, Metschnikowia sp., Rhodotorula sp. and Rhodosporidium toruloides were grown under nitrogen-limited conditions with crude glycerol employed as substrate in shake flasks, presenting interesting dry cell weight (DCW) production. Three of these strains belonging to Metschnikowia sp. accumulated significant quantities of endopolysaccharides (i.e. the strain V.V.-D4 produced 11.0 g/L of endopolysaccharides, with polysaccharides in DCW ≈ 63% w/w). A total of six Y. lipolytica strains produced either citric acid or mannitol. Most of the screened yeasts presented somehow elevated lipid and polysaccharides in DCW values at the early steps of growth despite nitrogen appearance in the fermentation medium. Lipid in DCW values decreased as growth proceeded. R. toruloides DSM 4444 cultivated on media presenting higher glycerol concentrations presented interesting lipid-accumulating capacities (maximum lipid = 12.5 g/L, maximum lipid in DCW = 43.0-46.0% w/w, conversion yield on glycerol = 0.16 g/g). Replacement of crude glycerol by xylose resulted in somehow decreased lipid accumulation. In xylose/glycerol mixtures, xylose was more rapidly assimilated from glycerol. R. toruloides total lipids were mainly composed of triacylglycerols. Total cellular fatty acid composition on xylose presented some differences compared with that on glycerol. Cellular lipids contained mainly oleic and palmitic acid.

High-added value products from microalgae and prospects of aquaculture wastewaters as microalgae growth media.

Abstract: Aquaculture plays an important role in human nutrition and economic development but is often expanded to the detriment of the natural environment. Several research projects, aimed at cultivating microalgae in aquaculture wastewaters (AWWs) to reduce organic loads and minerals, along with the production of microalgal cell mass and metabolic products, are underway. Microalgal cell mass is of high nutritional value and is regarded as a candidate to replace, partially at least, the fish meal in the fish feed. Also, microalgal cell mass is considered as a feedstock in the bio-fuel manufacture, as well as a source of high-added value metabolic products. The production of these valuable products can be combined with the reuse of AWWs in the light of environmental concerns related with the aquaculture sector. Many research papers published in the last decade demonstrate that plenty of microalgae species are able to efficiently grow in AWWs, mainly derived from fish and shrimp farms, and produce valuable metabolites reducing the AWW pollutant load. We conclude that bio-remediation of AWWs combining with the production of microalgae cell mass and specific metabolites is probably the most convenient and economical solution for AWWs management and can contribute to the sustainable growth of the aquaculture.

Methanogenic archaea in peatlands.

Abstract: Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.

Long-term combined administration of Bifidobacterium bifidum TMC3115 and Lactobacillus plantarum 45 alleviates spatial memory impairment and gut dysbiosis in APP/PS1 mice

Abstract: This study aimed to determine the effects of Bifidobacterium bifidum TMC3115, Lactobacillus plantarum 45 (LP45) and their combined use on cognitive performance and gut microbiota in APP/PS1 mice. The APP/PS1 mice were randomly divided into four groups: Alzheimer's disease (AD) model group, TMC3115 group [1 × 109 colony forming unit (CFU)], LP45 group (1 × 109 CFU) and a mixture group of TMC3115 (5 × 108 CFU) and LP45 (5 × 108 CFU). The wild-type littermates were chosen as normal control. The mice were sacrificed at the end of 22 weeks after behavioral evaluation. Collected cecum content was analyzed using 16S rRNA sequencing. Combined use of TMC3115 and LP45 significantly increased the times across the platform, time spent in the target quadrant compared with the AD, TMC3115 and LP45 groups in Morris water maze test. Microbiota analysis showed that combined TMC3115 and LP45 supplementation significantly increased observed species and beta diversity, and reversed gut dysbiosis by decreasing the abundance of Bacteroides and increasing the abundance of Acetatifactor and Millionella. These results indicate the long-term combined administration of TMC3115 and LP45 can improve spatial memory impairment in APP/PS1 mice and suggest that modifying the gut microbiome may provide potential benefits for AD patients.

Improving Alzheimer's disease by altering gut microbiota in tree shrews with ginsenoside Rg1

Abstract: Ginsenoside Rg1 (GRg1) has neuroprotective effects on Alzheimer's disease (AD). The occurrence and progression of AD are closely related to gut microbiota. Few studies have learned the direct relationship between GRg1 and gut microbiota. In this study, we found an original way to research this relationship by using GRg1 in the AD model of tree shrews. Morris water maze and immunohistochemistry were performed to test the cognition repairing function of GRg1 by tree shrews and 16S ribosomal RNA sequencing was used to explore the composition and abundance of gut microbiota. After GRg1 treatment, the result of Morris water maze showed an improvement in cognitive function, and immunohistochemistry revealed a decrease in tau protein. Moreover, 16SrRNA sequencing results showed the abundances of Proteobacteria and Verrucomicrobia were significantly different, and Lactobacillaceae was significantly increased in the GRg1 treatment group. It also showed that the gut microbiome with middle and high doses of GRg1 was close to the normal group. In conclusion, this study suggests that GRg1 at middle and high doses may change the abundance of gut microbiota to improve AD, and thatProteobacteria and Verrucomicrobia are key microbiota. This is the first report that has ever studied the relationship between GRg1 and gut microbiota in tree shrews.

Glyphosate-based herbicide affects the composition of microbes associated with Colorado potato beetle (Leptinotarsa decemlineata)

Abstract: Here, we examined whether glyphosate affects the microbiota of herbivores feeding on non-target plants. Colorado potato beetles (Leptinotarsa decemlineata) were reared on potato plants grown in pots containing untreated soil or soil treated with glyphosate-based herbicide (GBH). As per the manufacturer's safety recommendations, the GBH soil treatments were done 2 weeks prior to planting the potatoes. Later, 2-day-old larvae were introduced to the potato plants and then collected in two phases: fourth instar larvae and adults. The larvae's internal microbiota and the adults' intestinal microbiota were examined by 16S rRNA gene sequencing. The beetles' microbial composition was affected by the GBH treatment and the differences in microbial composition between the control and insects exposed to GBH were more pronounced in the adults. The GBH treatment increased the relative abundance of Agrobacterium in the larvae and the adults. This effect may be related to the tolerance of some Agrobacterium species to glyphosate or to glyphosate-mediated changes in potato plants. On the other hand, the relative abundances of Enterobacteriaceae, Rhodobacter, Rhizobium and Acidovorax in the adult beetles and Ochrobactrum in the larvae were reduced in GBH treatment. These results demonstrate that glyphosate can impact microbial communities associated with herbivores feeding on non-target crop plants.

New ECCO model documents for Material Deposit and Transfer Agreements in compliance with the Nagoya Protocol

Abstract: The European Culture Collections' Organisation presents two new model documents for Material Deposit Agreement (MDA) and Material Transfer Agreement (MTA) designed to enable microbial culture collection leaders to draft appropriate agreement documents for, respectively, deposit and supply of materials from a public collection. These tools provide guidance to collections seeking to draft an MDA and MTA, and are available in open access to be used, modified, and shared. The MDA model consists of a set of core fields typically included in a 'deposit form' to collect relevant information to facilitate assessment of the status of the material under access and benefit sharing (ABS) legislation. It also includes a set of exemplary clauses to be included in 'terms and conditions of use' for culture collection management and third parties. The MTA model addresses key issues including intellectual property rights, quality, safety, security and traceability. Reference is made to other important tools such as best practices and code of conduct related to ABS issues. Besides public collections, the MDA and MTA model documents can also be useful for individual researchers and microbial laboratories that collect or receive microbial cultures, keep a working collection, and wish to share their material with others.

Methanobactin from methanotrophs: genetics, structure, function and potential applications.

Abstract: Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

Direct antibacterial and antibiotic resistance modulatory activity of chalcones synthesized from the natural product 2-hydroxy-3,4,6-trimethoxyacetophenone.

Abstract: Antibiotic for clinical use lose its effectiveness over time due to bacterial resistance. In this work, four chalcones with modifications in their ligands were synthesized from the natural product 2-hydroxy-3,4,6-trimethoxyacetophenone, characterized by nuclear magnetic resonance (NMR) and infrared spectroscopy, and tested in bacterial models to investigate the direct and modifiers effects of the antibiotic activity of these four novel chalcones. The tests followed the broth microdilution methodology to obtain the Minimum Inhibitory Concentration (MIC). The MIC/8 of the products were used in the resistance reversion test. The chalcone 2 showed the best result in terms of direct activity, with MIC 645 μg/mL for Staphylococcus aureus and 812 μg/mL for Escherichia coli. While, for the bacterial resistance reversal test, the chalcones presented several synergistic interactions, being that chalcone 4 had the best interaction with the tested antibiotics. It was found that the type of ligand, as well as its position in the ring, interferes in the modulation of the antibiotic activity. Our results show that chalcones are strong candidates to be used as antibacterial drug or in combination with antibiotics for the treatment of infections caused by multidrug-resistant (MDR) strains.

Successful enrichment of low-abundant comammox Nitrospira from nitrifying granules under ammonia-limited conditions.

Abstract: In artificial engineered systems, nitrification is a key reaction that accounts for the removal of biological nitrogen. Recently, a single microbe capable of oxidizing ammonia to nitrate, known as a complete ammonia oxidizer (comammox), has been discovered. Although the abundance and diversity of comammox Nitrospira in engineered systems have been identified through molecular-based approaches, the enrichment and isolation of comammox Nitrospira remains a challenge. Therefore, the aim of this study was to enrich comammox Nitrospira from nitrifying granules, which were used to increase the efficiency of biological nitrogen removal in wastewater treatment plants. We sought to accomplish this through the use of a fixed-bed continuous feeding bioreactor. Fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing and qPCR of functional genes were utilized to monitor the growth of nitrifiers including comammox Nitrospira. Cloning of comammox amoA genes identified amoA phylogeny of enriched comammox Nitrospira. This work is an example demonstrating that continuous supply of low ammonium concentrations alongside biomass carriers is effective in cultivating comammox Nitrospira from engineered systems.

Membrane transporters in the bioproduction of organic acids: state of the art and future perspectives for industrial applications.

Abstract: Organic acids such as monocarboxylic acids, dicarboxylic acids or even more complex molecules such as sugar acids, have displayed great applicability in the industry as these compounds are used as platform chemicals for polymer, food, agricultural and pharmaceutical sectors. Chemical synthesis of these compounds from petroleum derivatives is currently their major source of production. However, increasing environmental concerns have prompted the production of organic acids by microorganisms. The current trend is the exploitation of industrial biowastes to sustain microbial cell growth and valorize biomass conversion into organic acids. One of the major bottlenecks for the efficient and cost-effective bioproduction is the export of organic acids through the microbial plasma membrane. Membrane transporter proteins are crucial elements for the optimization of substrate import and final product export. Several transporters have been expressed in organic acid-producing species, resulting in increased final product titers in the extracellular medium and higher productivity levels. In this review, the state of the art of plasma membrane transport of organic acids is presented, along with the implications for industrial biotechnology.

Indole signaling decreases biofilm formation and related virulence of Listeria monocytogenes.

Abstract: Bacterial communication system known as quorum sensing (QS) is a pivotal system for bacterial survival, adaptation and pathogenesis. Members in the multicellular community may synthesize or acquire a signaling molecule in order to elicit downstream cellular processes. Roles of indole and derivatives, a new class of quorum-sensing signal molecules, in various bacterial physiologies and virulence have been reported recently. Indole is normally found in mammal gastrointestinal tract as a metabolite of tryptophan metabolism by microbiota. Therefore, interspecies connection via indole signaling among commensal bacteria and enteric pathogens could be anticipated. Effects of indole exposure on the virulence of Listeria monocytogenes were investigated by phenotypic and molecular approaches. Results demonstrated that synthetic indole and indole-rich conditioned medium significantly diminished biofilm formation and related virulence of L. monocytogenes including motility, cell aggregation and exopolysaccharide production. Transcript levels of virulence-associated (pssE, dltA, flaA, fliI, motB, agrA and hly) and regulatory genes (codY, sigB, prfA and gmaR) were substantially downregulated in indole-treated cells. Only mogR gene encoding for a repressor of motility genes was upregulated after indole exposure. Our findings raise the possibility that L. monocytogenes may acquire indole signaling from gut microbiota for resource-effective adaptation upon transition to new environment.

Characterization and bioremediation potential of nickel-resistant endophytic bacteria isolated from the wetland plant Tamarix chinensis.

Abstract: Wetlands have been proposed as a sink for pollutants such as heavy metals. Wetland plants play a significant role in the phytoremediation of heavy metals. Here, we isolated and characterized three novel nickel (Ni)-resistant endophytic bacteria (NiEB) from the wetland plant Tamarix chinensis. The NiEB were identified as Stenotrophomonas sp. S20, Pseudomonas sp. P21 and Sphingobium sp. S42. All isolates tolerated 50 mg L-1 Ni, with isolates S20 and P21 being more tolerant to Ni at up to 400 mg L-1. Moreover, isolate S42 removed 33.7% of nickel sulfate from the water by forming white precipitates. The three isolates exhibited different plant growth-promoting (PGP) traits related to the production of indole acetic acid (IAA), siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Phytotoxicity studies revealed that the growth of the wetland plants in a high Ni concentration (200 mg L-1) recovered after co-incubation with isolate S42. Overall, this study presents the first report of NiEB isolation from wetland plants and provides novel insights into the diverse functions of endophytic bacteria in a plant host with the potential to improve Ni phytoremediation.

Compilation of Escherichia coli K-12 outer membrane phage receptors - their function and some historical remarks.

Abstract: Many Escherichia coli phages have been sequenced, but in most cases their sequences alone do not suffice to predict their host specificity. Analysis of phage resistant E. coli K-12 mutants have uncovered a certain set of outer membrane proteins and polysaccharides as receptors. In this review, a compilation of E. coli K12 phage receptors is provided and their functional characterization, often driven by studies on phage resistant mutants, is discussed in the historical context. While great progress has been made in this field thus far, several proteins in the outer membrane still await characterization as phage receptors.

The biosurfactants iturin, lichenysin and surfactin, from vaginally isolated lactobacilli, prevent biofilm formation by pathogenic Candida.

Abstract: Lactic acid bacteria (LAB), particularly lactobacilli, are major components of the vaginal microbiota. Lactobacilli are facultative anaerobes forming a critical line of defense against pathogenic microorganisms, including those forming biofilms, such as Candida spp. This study aimed to investigate the anti-adhesion capabilities of vaginal Lactobacillus isolates against biofilms formed by pathogenic Candida species. When the extracellular biosurfactant activities of culture supernatants from 120 Lactobacillus isolates were evaluated by the oil-spreading method, clear spreading zones were recognized. Biofilm formation was quantified by the crystal violet plate assay, and different isolates exhibited anti-adhesion activity that ranged from 65.6to 74.4% inhibition against Candida spp. biofilms. Liquid chromatography high-resolution electrospray ionization mass spectrometry (LC-HRESIMS) identified biosurfactants, extracted from three representative Lactobacillus isolates, as surfactin, iturin and lichenysin. Finally, the distribution of representative genes from six different biosynthetic clusters, related to the production of different biosurfactants, was investigated by the polymerase chain reaction. In conclusion, surfactin, iturin and lichenysin were identified for the first time in vaginal Lactobacillus spp. These biosurfactants, which showed strong anti-adherence activity may be used as promising antibiofilm agents in equipment care to prevent vaginal infections by pathogenic Candida spp. with the prospect of reducing nosocomial infections.

Aerobic microbial communities in the sediments of a marine oxygen minimum zone

Abstract: The ecology of aerobic microorganisms is never explored in marine oxygen minimum zone (OMZ) sediments. Here we reveal aerobic bacterial communities along ∼3 m sediment-horizons of the eastern Arabian Sea OMZ. Sulfide-containing sediment-cores retrieved from 530 mbsl (meters beneath the sea-level) and 580 mbsl were explored at 15-30 cm intervals, using metagenomics, pure-culture-isolation, genomics and metatranscriptomics. Genes for aerobic respiration, and oxidation of methane/ammonia/alcohols/thiosulfate/sulfite/organosulfur-compounds, were detected in the metagenomes from all 25 sediment-samples explored. Most probable numbers for aerobic chemolithoautotrophs and chemoorganoheterotrophs at individual sample-sites were up to 1.1 × 107 (g sediment)-1. The sediment-sample collected from 275 cmbsf (centimeters beneath the seafloor) of the 530-mbsl-core yielded many such obligately aerobic isolates belonging to Cereibacter, Guyparkeria, Halomonas, Methylophaga, Pseudomonas and Sulfitobacter which died upon anaerobic incubation, despite being provided with all possible electron acceptors and fermentative substrates. High percentages of metatranscriptomic reads from the 275 cmbsf sediment-sample, and metagenomic reads from all 25 sediment-samples, matched the isolates' genomic sequences including those for aerobic metabolisms, genetic/environmental information processing and cell division, thereby illustrating the bacteria's in-situ activity, and ubiquity across the sediment-horizons, respectively. The findings hold critical implications for organic carbon sequestration/remineralization, and inorganic compounds oxidation, within the sediment realm of global marine OMZs.

Probiotic antigenotoxic activity as a DNA bioprotective tool: a minireview with focus on endocrine disruptors.

Abstract: Nowadays, the interest in the role of dietary components able to influence the composition and the activity of the intestinal microbiota and, consequently, to modulate the risk of genotoxicity and colon cancer is increasing in the scientific community. Within this topic, the microbial ability to have a protective role at gastrointestinal level by counteracting the biological activity of genotoxic compounds, and thus preventing the DNA damage, is deemed important in reducing gut pathologies and is considered a new tool for probiotics and functional foods. A variety of genotoxic compounds can be found in the gut and, besides food-related mutagens and other DNA-reacting compounds, there is a group of pollutants commonly used in food packaging and/or in thousands of everyday products called endocrine disruptors (EDs). EDs are exogenous substances that alter the functions of the endocrine system through estrogenic and anti-estrogenic activity, which interfere with normal hormonal function in human and wildlife. Thus, this paper summarizes the main applications of probiotics, mainly lactobacilli, as a bio-protective tool to counteract genotoxic and mutagenic agents, by biologically inhibiting the related DNA damage in the gut and highlights the emerging perspectives to enlarge and further investigate the microbial bio-protective role at intestinal level.

Spent mushroom substrate for a second cultivation cycle of Pleurotus mushrooms and dephenolization of agro-industrial wastewaters.

Abstract: Spent mushroom substrate (SMS) of Pleurotus ostreatus was supplemented with wheat bran and soybean flour and used as substrate for a new cultivation cycle of the oyster mushrooms Pleurotus ostreatus and Pleurotus pulmonarius. The bioconversion efficiency of mushrooms produced over substrate (BE%) used and the chemical composition of sporophores were evaluated. The concentration of mycelial mass, crude exopolysaccharide content and laccase enzyme activity were also determined at the supplemented SMS before inoculation, at 50% and 100% of colonization stages in the new cultivation and in the final re-utilized SMS. The laccase enzyme was extracted to examine SMS potential for the dephenolization of olive mill and winery wastewaters. Results showed that both Pleurotus species exhibited BE over 185%, demonstrating this bioprocess could represent a promising strategy to convert SMS into nutritional food. Data also indicate the strong positive impact that SMS could have in the solid wastes' management and agribusiness enhancement.

Dissolved organic matter stimulates N2 fixation and nifH gene expression in Trichodesmium

Abstract: Mixotrophy, the combination of heterotrophic and autotrophic nutrition modes, is emerging as the rule rather than the exception in marine photosynthetic plankton. Trichodesmium, a prominent diazotroph ubiquitous in the (sub)tropical oceans, is generally considered to obtain energy via autotrophy. While the ability of Trichodesmium to use dissolved organic phosphorus when deprived of inorganic phosphorus sources is well known, the extent to which this important cyanobacterium may benefit from other dissolved organic matter (DOM) resources is unknown. Here we provide evidence of carbon-, nitrogen- and phosphorus-rich DOM molecules enhancing N2 fixation rates and nifH gene expression in natural Trichodesmium colonies collected at two stations in the western tropical South Pacific. Sampling at a third station located in the oligotrophic South Pacific Gyre revealed no Trichodesmium but showed presence of UCYN-B, although no nifH expression was detected. Our results suggest that Trichodesmium behaves mixotrophically in response to certain environmental conditions, providing them with metabolic plasticity and adding up to the view that mixotrophy is widespread among marine microbes.

Conversion of waste materials into very long chain fatty acids by the recombinant yeast Yarrowia lipolytica.

Abstract: Erucic acid (C22:1Δ13) has several industrial applications including its use as a lubricant, surfactant and biodiesel and composite material constituent. It is produced by plants belonging to the Brassicaceae family, especially by the high erucic acid rapeseed. The ability to convert oleic acid into erucic acid is facilitated by FAE1. In this study, FAD2 (encoding Δ12-desaturase) was deleted in the strain Po1d to increase oleic acid content. Subsequently, FAE1 from Thlaspi arvense was overexpressed in Yarrowia lipolytica with the Δfad2 genotype. This resulted in the YL10 strain producing very long chain fatty acids, especially erucic acid. The YL10 strain was cultivated in media containing crude glycerol and waste cooking oil as carbon substrates. The cells grown using glycerol produced microbial oil devoid of linoleic acid, which was enriched with very long chain fatty acids, mainly erucic acid (9% of the total fatty acids). When cells were grown using waste cooking oil, the highest yield of erucic acid was obtained (887 mg L-1). However, external linoleic and α-linolenic were accumulated in cellular lipids when yeasts were grown in an oil medium. This study describes the possibility of conversion of waste material into erucic acid by a recombinant yeast strain.

A toddler SHIME® model to study microbiota of young children

Abstract: The 'first 1000 days of life' determine the gut microbiota composition and can have long-term health consequences. In this study, the simulator of the human intestinal microbial ecosystem (SHIME®) model, which represents the main functional sections of the digestive tract, was chosen to study the microbiota of young children. The aim of this study was to reproduce the digestive process of toddlers and their specific colonic environment. The ascending, transverse and descending colons of SHIME® model were inoculated with feces from three donors aged between 1 and 2 years-old, in three separate runs. For each run, samples from colon vessels were collected at days 14, 21 and 28 after microbiota stabilization period. Short chain fatty acid concentrations determined by HPLC showed that microbiota obtained in SHIME® model shared characteristics between adults and infants. In addition, microbial diversity and bacterial populations determined by 16S rRNA amplicon sequencing were specific to each colon vessel. In conclusion, the SHIME® model developed in this study seemed well adapted to evaluate prebiotic and probiotic impact on the specific microbiota of toddlers, or medicine and endocrine disruptor metabolism. Moreover, this study is the first to highlight some biofilm development in in vitro gastrointestinal modelling systems.

Prevalence, antibiotic susceptibility and characterization of Vibrio parahaemolyticus isolates in China

Abstract: Vibrio parahaemolyticus is a marine and estuarine bacterium that poses a major threat to human health worldwide. In this study, from 2017 to 2019, we evaluated 900 food samples collected from China in 2017, with the aim of determining the incidence and features of V. parahaemolyticus in ready-to-eat (RTE) foods, shrimp and fish in China. The contamination rates in these were 3.67, 19.33 and 10.67%, respectively, and the prevalence of V. parahaemolyticus was higher in summer than in winter. In addition, 101 V. parahaemolyticus strains were isolated. Our results suggested that most of the isolates were resistant to aminoglycosides based on the antimicrobial resistance patterns of these aquatic product isolates against 14 antimicrobial agents. Furthermore, most of the isolates were multidrug-resistant. Serotyping showed that the isolates of the O2 serotype comprised the maximum proportion. Enterobacterial repetitive intergenic consensus sequence (ERIC)-PCR results indicated that the isolates (n = 101) could be classified into 12 clusters. There were 82 STs suggesting genetic variation and relatedness among these isolates. Our findings demonstrated the presence of V. parahaemolyticus in foods from Chinese retail markets and show that this methodology can be used for microbiological risk assessment in China.

Mathematical modeling of the 'inoculum effect': six applicable models and the MIC advancement point concept.

Abstract: Antimicrobial treatment regimens against bacterial pathogens are designed using the drug's minimum inhibitory concentration (MIC) measured at a bacterial density of 5.7 log10(colony-forming units (CFU)/mL) in vitro. However, MIC changes with pathogen density, which varies among infectious diseases and during treatment. Incorporating this into treatment design requires realistic mathematical models of the relationships. We compared the MIC-density relationships for Gram-negative Escherichia coli and non-typhoidal Salmonella enterica subsp. enterica and Gram-positive Staphylococcus aureus and Streptococcus pneumonia (for n = 4 drug-susceptible strains per (sub)species and 1-8 log10(CFU/mL) densities), for antimicrobial classes with bactericidal activity against the (sub)species: β-lactams (ceftriaxone and oxacillin), fluoroquinolones (ciprofloxacin), aminoglycosides (gentamicin), glycopeptides (vancomycin) and oxazolidinones (linezolid). Fitting six candidate mathematical models to the log2(MIC) vs. log10(CFU/mL) curves did not identify one model best capturing the relationships across the pathogen-antimicrobial combinations. Gompertz and logistic models (rather than a previously proposed Michaelis-Menten model) fitted best most often. Importantly, the bacterial density after which the MIC sharply increases (an MIC advancement-point density) and that density's intra-(sub)species range evidently depended on the antimicrobial mechanism of action. Capturing these dependencies for the disease-pathogen-antimicrobial combination could help determine the MICs for which bacterial densities are most informative for treatment regimen design.

Screening of bacterial strains from the gut of Pacific White Shrimp (Litopenaeus vannamei) and their efficiencies in improving the fermentation of soybean meal

Abstract: Microbial fermentation is an efficient, economical and eco-friendly approach to overcome the limitations in soybean meal replacement of fish meal in aquaculture. However, little research focused on the development of shrimp-derived strains for fermentation of SBM. In this study, Bacillus sanfensis (SQVG18) and Bacillus stratosphericus (SQVG22) were screened from shrimp intestine for fermentation according to the activities of protease, cellulase and phytase. The optimized fermentation conditions of SQVG18 and SQVG22 were as follow: fermentation temperature (40°C vs 35°C), fermentation time (48h both), inoculation amount [4% both (v/m)], solid-liquid ratio [1:1.2 vs 1:1 (g/ml)]. After 48 h fermentation, SQVG18 and SQVG22 increased crude protein content by 6.93% and 5.95%, respectively; degraded most of macromolecular proteins to micromolecular proteins (< 20 kDa); improved amino acids profiles, like lysine and methionine in particular; significantly decreased the anti-nutritional factors such as trypsin inhibitor, glycinin and β-conglycinin (P < 0.05). In addition, both strains were observed no hemolytic activity, less antibiotic resistance genes and definite inhibition to common shrimp pathogens of Vibrio alginolyticus sp. and Vibrio parahaemolyticus sp. These results indicated that both strains could improve nutrition values of soybean meal effectively and have potential applications in shrimp culture.

The influence of diet on the microbiota of live-feed rotifers (Brachionus plicatilis) used in commercial fish larviculture

Abstract: Live-feed is indispensable to commercial fish larviculture. However, high bacterial loads in rotifers could pose a biosecurity risk. While this may be true, live-feed associated bacteria could also be beneficial to fish larvae through improved feed utilization or pathogen inhibition following host microbiota modification. The study objective was to elucidate the largely unexplored microbiota of rotifers propagated on five different diets through bacterial community profiling by 16S rRNA gene amplicon sequencing. Investigated rotifer samples had a median observed alpha-diversity of 338 ± 87 bacterial species. Alpha- and Gamma-Proteobacteria dominated the rotifer microbiota followed by members of classes Flavobacteriia, Cytophagia, Mollicutes, Phycisphaerae and Bacteroidia. Different diets significantly altered the bacterial communities associated with rotifers according to PERMANOVA test results and beta dispersion calculations. A common core rotifer microbiome included 31 bacterial species present in relative abundances over 0.01%. We discuss the functional role of some microbiome members. Our data suggested the presence of several known fish pathogens in stock rotifers. However, we found no evidence for increased loads of these presumptive taxa in propagated live-feed rotifers during this field trial.

Diatom DNA barcodes for forensic discrimination of drowning incidents.

Abstract: The presence of diatoms in victim's internal organs has been regarded as a gold biological evidence of drowning. The idea becomes true at the advent of DNA metabarcoding. Unfortunately, the DNA barcode of diatoms are far from being applicable due to neither consensus on the barcode and nor reliable reference library.In this study we tested 23 pairs of primers, including two new primer pairs, Baci18S (V4 of 18S) and BacirbcL (central region of rbcL), for amplifying fragments of 16S/18S, 23S/28S, COI, ITS and rbcL. A total of five pairs of primers performed satisfactory for diatoms. We used three of them, 18S605 (V2 + V3 of 18S), Baci18S and BacirbcL, to barcode four water samples using next generation sequencing platform. The results showed that these primers worked well for NGS metabarcoding of diatoms. We suggest that 18S605, Baci18S and BacirbcL be barcodes of diatoms and the corresponding primer pairs be used. Considering a quite high proportion of sequences deposited in GenBank were mislabeled, the most urgent task for DNA barcoding of diatoms is to create standard sequences using correctly identified specimens, ideally type specimens.