Environmental Microbiota Research Articles

Intestinal Anti-Inflammatory Activity of the Aqueous Extract from Ipomoea asarifolia in DNBS-Induced Colitis in Rats.

Inflammatory bowel disease is triggered by an uncontrolled immune response associated with genetic, environmental, and intestinal microbiota imbalance. Ipomoea asarifolia (IA), popularly known as “salsa” or “brave salsa”, belongs to the Convolvulaceae family. The aim of this approach was to study the preventive effect of IA aqueous extract in 2,4-dinitrobenzene sulfonic acid (DNBS)-induced colitis in rats. Rats pretreated with IA extract or sulfasalazine (SSZ) received intracolonic instillation of DNBS in 50% ethanol (v/v). IA extract presented a protective effect against intestinal inflammation, with improvement in the disease activity index and macroscopic damage. IA or SSZ significantly reduced myeloperoxidase activity, and also down-regulation of the gene expression of JNK1, NF-κβ-p65, STAT3, and decreased levels of TNFα, IL-1β, and increased IL-10, associated with a significant improvement of oxidative stress, in addition to a reduction in MDA and an increase of glutathione in colonic tissue. The protective effect of the extract was also confirmed in histological evaluation, showing preservation of the colonic cytoarchitecture. Immunohistochemical analysis revealed down-regulation of NF-κβ-p65, iNOS, IL-17, and up-regulation of SOCs-1 and MUC-2. IA extract presents antioxidant and anti-inflammatory intestinal properties, and proved to be a potential application for preventing damage induced by DNBS.

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment

Environmental microbiota plays important roles in the intestinal microbiota of aquatic animals. The Pacific white shrimp with high commercial value and euryhaline property has become the most important commercial species of shrimp in the world. However, the association between shrimp intestine and sediment at freshwater and marine cultured environment should be investigated to reveal the microbiota differences. In the present study, Miseq sequencing technology and bioinformatics were used to comprehensively compare the bacterial communities and all samples' V3–V4 regions of 16S rRNA gene were sequenced. Results showed that 55 phyla and 789 genera were identified due to the classifiable sequence. Sequencing data demonstrated statistically significant diverse microbiota compositions in the shrimp intestine and sediment at freshwater and marine cultured environment at the phylum and genus level. At the phylum level, the dominant phyla in all groups were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, Cyanobacteria, Bacteroidetes, Acidobacteria, Verrucomicrobia, Saccharibacteria. Proteobacteria were the most abundant and largest phylum except in the intestine of marine cultured shrimp and Actinobacteria may be enriched in the shrimp intestine from sediment. At the genus level, nine out of the twelve dominant genera exhibited statistically significant differences among all groups. Moreover, Lactobacillus tend to be enriched in the freshwater cultured shrimp intestine, while Synechococcus and Vibrio extremely abundance in the marine cultured shrimp intestine. These results showed that the bacterial compositions are mostly the same in shrimp intestine and sediment, while with different relative abundances of the bacterial communities. In conclusion, this study may greatly enhance our understanding of the microbiota characteristics between shrimp and sediment. Moreover, it provided guidance for the healthy aquaculture at freshwater and marine cultured environment.

Contamination by perfluoroalkyl substances and microbial community structure in Pearl River Delta sediments

Environmental microbiota play essential roles in the maintenance of many biogeochemical processes, including nutrient cycling and pollutant degradation. They are also highly susceptible to changes in environmental stressors, with environmental pollutants being key disruptors of microbial dynamics. In the present study, a scientific cruise was launched on July 2017 around Pearl River Delta, a suitable studying site for perfluoroalkyl substances (PFASs) in the wake of the severe PFAS pollution. Surface sediment samples were collected from 18 representative stations to assess PFAS accumulation and profile microbial community. PFAS concentrations ranged from 24.2 to 181.4 pg/g dry weight in sediment, and perfluorooctanesulfonic acid (PFOS) was the dominant homologue. The concentrations of PFAS homologues in the current study were much lower than those reported in previous studies, implying effective management and control of pollution from PFAS-related industries. 16S rRNA gene amplicon sequencing revealed that Proteobacteria was the dominant phylum, while nitrogen-metabolizing Nitrosopumilus and sulfate-reducing Desulfococcus genera were the most abundant. Variations in microbial communities among sampling stations were mainly due to the differences in abundances of Escherichia, Nitrosopumilus, and Desulfococcus. The outbreak of Escherichia bacteria at specific coastal stations potentially indicated the discharge of fecal matter into the marine environment. Dissolved oxygen (DO) in bottom seawater significantly influenced the structure of microbial communities in the sediment, while current study failed to observe significant effects from PFAS pollutants. Positive correlations were found between DO and sulfate-reducing bacteria in Desulfococcus and GOUTA19 genera. Overall, this study explored relationships between environmental variables (e.g., PFAS pollutants) and sediment bacteria. Biogeochemical parameters significantly influenced the structure and composition of microbial communities in sediment.

Diet-induced shifts in the crown-of-thorns (Acanthaster sp.) larval microbiome

Predation by the crown-of-thorns seastar (CoTS; Acanthaster sp.) is a pervasive stressor attributing to the decline of coral reefs. These outbreaks are suggested to be linked to eutrophy-driven recruitment pulses, where increased nutrients enhance larval success. CoTS larvae, however, are tolerant of oligotrophic conditions typical of tropical ecosystems and outbreaks occur in regions isolated from eutrophy, highlighting the resilience of these larvae to oligotrophic conditions. Here, we test the hypothesis that CoTS larvae associate with bacterial communities that are dynamic across an oligotrophic–eutrophic continuum and are specific to each feeding regime. Our analysis of the CoTS larval microbiome suggests that CoTS larvae associate with a bacterial community distinct from the environmental microbiota and that this community experiences a community-level shift in response to differential feeding that is maintained over development. Symbioses with a diverse and dynamic, and a potentially phototrophic, bacterial community may contribute to resilience of CoTS larvae that enable the success of CoTS and, perhaps, other tropical marine larvae in oligotrophic seas.

Associations between the gut microbiota and host responses to high altitude.

Hypobaric hypoxia and dietary protein and fat intakes have been independently associated with an altered gastrointestinal (GI) environment and gut microbiota, but little is known regarding host-gut microbiota interactions at high altitude (HA) and the impact of diet macronutrient composition. This study aimed to determine the effect of dietary protein:fat ratio manipulation on the gut microbiota and GI barrier function during weight loss at high altitude (HA) and to identify associations between the gut microbiota and host responses to HA. Following sea-level (SL) testing, 17 healthy males were transported to HA (4,300 m) and randomly assigned to consume provided standard protein (SP; 1.1 g·kg−1·day−1, 39% fat) or higher protein (HP; 2.1 g·kg−1·day−1, 23% fat) carbohydrate-matched hypocaloric diets for 22 days. Fecal microbiota composition and metabolites, GI barrier function, GI symptoms, and acute mountain sickness (AMS) severity were measured. Macronutrient intake did not impact fecal microbiota composition, had only transient effects on microbiota metabolites, and had no effect on increases in small intestinal permeability, GI symptoms, and inflammation observed at HA. AMS severity was also unaffected by diet but in exploratory analyses was associated with higher SL-relative abundance of Prevotella, a known driver of interindividual variability in human gut microbiota composition, and greater microbiota diversity after AMS onset. Findings suggest that the gut microbiota may contribute to variability in host responses to HA independent of the dietary protein:fat ratio but should be considered preliminary and hypothesis generating due to the small sample size and exploratory nature of analyses associating the fecal microbiota and host responses to HA.NEW & NOTEWORTHY This study is the first to examine interactions among diet, the gut microbiota, and host responses to weight loss at high altitude (HA). Observed associations among the gut microbiota, weight loss at HA, and acute mountain sickness provide evidence that the microbiota may contribute to variability in host responses to HA. In contrast, dietary protein:fat ratio had only minimal, transient effects on gut microbiota composition and bacterial metabolites which were likely not of clinical consequence.

Analysis of intestinal microbial composition and function of mother-infant pairs by single cell amplification technique

Microorganism plays an important role in human health, such as promoting digestion and absorption, regulating the host immune system, maintaining dental health, and resistance to pathogens invasion. The microbes of newborn babies are crucial to their health; it may be involved in infant brain development and neurodevelopment. Maternal genotype and diet, antibiotic use, maternal viral infections during pregnancy and mode of delivery are possible factors that can modulate the intestinal microbiome. Our previous studies have found that microbes can be vertically transferred from mother to infant through two main ways, birth canal and the breast milk. In the natural environment, only 1% of the microbes can be cultured. Thus, many low and non-cultivatable taxa cannot be accurately identified by traditional methods. Comparing with PCR-based whole genome amplification methods, the single cell multiple replacement amplification (MDA) technique can reduce amplification bias by 3~4 orders of magnitude, increase the minimal DNA of a single bacterial cell by about 5 billion times, and produce an average length of >12 kb amplification, which allows the gene fragment to be sequenced accurately. In this experiment, we applied the single-cell amplification technique to analyze 3 pairs of maternal and infant feces (a total of 48 bacterial suspensions) in order to explore the composition of intestinal microorganisms and analyze the related functional genes. The results showed that the fecal microorganisms of each pair of mother and infant were highly similar (>99%) despite in different abundance. Among three infants, one vaginally born infant showed similar high abundance species to its mother, such as Roseburia hominis , Roseburia intestinalis , Eubacterium Rectale , and Eubacterium eligens , while the high abundant species of other two C-sections infants were associated with the skin and mouth, such as Propionibacterium acnes , Staphylococcus saprophyticus , Haemolyticus , and Delftia Acidovorans . Bacteroides ( B. ), such as B. fragilis , B. helcogenes , and B. salanitronis , were less prevalent in C-section delivered infants compared to the vaginally born infant. A total of 1283 bacterial species were identified in this study. In addition to the previously reported human gut-related species, we detected three low-abundant taxa, namely Lactobacillus ( L .) amylovorus , L. kefiranofaciens , L. sanfranciscensis , and Bifidobacterium asteroids . The functional metagenomes of fecal samples showed that the carbohydrate-related phosphotransferase system (PTS) genes and beta-glucoside genes were enriched in the infant microbiome. In this study, we applied the single-cell amplification technique to explore the composition and function of intestinal microorganisms of the mother and infant, with high sequencing depth and species diversity coverage. We also detected some low abundance species, which were rarely reported before. We believe the present approach is suitable for future analysis of microbiota of different ecological environments.

Molecular Variances Between Right- and Left-sided Colon Cancers

During the past few years, several important clinical and molecular differences have been observed simply based on anatomic tumor location of colorectal cancer. With this review, we aimed to give an updated overview of the recent findings on tumor location as a surrogate of embryological, molecular, and clinical differences that have a direct impact on our daily clinical practice. Increasing evidence has demonstrated a role for the microbiota in shaping inflammatory environments and promoting CRC growth and spread, and now we know that bacterial phylotypes vary depending on the primary tumor location. Compelling evidence has shown that tumor sidedness has both a strong prognostic and predictive value. In fact, right-sided colon cancers display a markedly worse prognosis compared to left-sided tumors; moreover, it seems that right-sided RAS wild-type metastatic colorectal cancer benefits from bevacizumab-based therapy while left-sided tumors have better outcomes with cetuximab-based treatment in the first-line setting. Since the underlying reasons of these differences are yet unknown, further investigations are warranted in this expanding and relevant field. In this review, we summarize the actual knowledge on the clinical, microbiome, and molecular differences observed between right- and left-sided colon cancers. We also present an overview of the existing data on the prognostic and predictive impact of tumor sidedness on metastatic colorectal cancer patient outcome.

Anthropogenic influence shapes the distribution of antibiotic resistant bacteria (ARB) in the sediment of Sundarban estuary in India

The abundance and dissemination of antibiotic resistance genes as emerging environmental contaminants have become a significant and growing threat to human and environmental health. Traditionally, investigations of antibiotic resistance have been confined to a subset of clinically relevant antibiotic-resistant bacterial pathogens. During the last decade it became evident that the environmental microbiota possesses an enormous number and diversity of antibiotic resistance genes, some of which are very similar to the genes circulating in pathogenic microbiota. Recent studies demonstrate that aquatic ecosystems are potential reservoirs of antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs). Therefore, these aquatic ecosystems serve as potential sources for their transmission of ARGs to human pathogens. An assessment of such risks requires a better understanding of the level and variability of the natural resistance background and the extent of the anthropogenic impact. We have analyzed eight sediment samples from Sundarban mangrove ecosystem in India, collected at sampling stations with different histories of anthropogenic influences, and analyzed the relative abundance of the blaTEM gene using quantitative real-time PCR. The blaTEM gene abundance strongly correlated with the respective anthropogenic influences (polyaromatic hydrocarbon, heavy metals etc.) of the sampling stations. Besides, 18 multidrug-resistant (ampicillin, kanamycin, vancomycin, and tetracycline resistant) bacterial strains (ARBs) were isolated and characterized. Moreover, the effect of different antibiotics on the biofilm forming ability of the isolates was evaluated quantitatively under a variety of experimental regimes. This is the first report of preservation and possible dissemination of ARGs in the mangrove ecosystem.

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes.

Environmental microbes have harbored the capacity for antibiotic production for millions of years, spanning the evolution of humans and other vertebrates. However, the industrial-scale use of antibiotics in clinical and agricultural practice over the past century has led to a substantial increase in exposure of these agents to human and environmental microbiota. This perturbation is predicted to alter the ecology of microbial communities and to promote the evolution and transfer of antibiotic resistance (AR) genes. We studied wild and captive baboon populations to understand the effects of exposure to humans and human activities (e.g., antibiotic therapy) on the composition of the primate fecal microbiota and the antibiotic-resistant genes that it collectively harbors (the "resistome"). Using a culture-independent metagenomic approach, we identified functional antibiotic resistance genes in the gut microbiota of wild and captive baboon groups and saw marked variation in microbiota architecture and resistomes across habitats and lifeways. Our results support the view that antibiotic resistance is an ancient feature of gut microbial communities and that sharing habitats with humans may have important effects on the structure and function of the primate microbiota. IMPORTANCE Antibiotic exposure results in acute and persistent shifts in the composition and function of microbial communities associated with vertebrate hosts. However, little is known about the state of these communities in the era before the widespread introduction of antibiotics into clinical and agricultural practice. We characterized the fecal microbiota and antibiotic resistomes of wild and captive baboon populations to understand the effect of human exposure and to understand how the primate microbiota may have been altered during the antibiotic era. We used culture-independent and bioinformatics methods to identify functional resistance genes in the guts of wild and captive baboons and show that exposure to humans is associated with changes in microbiota composition and resistome expansion compared to wild baboon groups. Our results suggest that captivity and lifestyle changes associated with human contact can lead to marked changes in the ecology of primate gut communities.

Bacterial microbiota assemblage in Aedes albopictus mosquitoes and its impacts on larval development.

Interactions between bacterial microbiota and mosquitoes play an important role in mosquitoes' capacity to transmit pathogens. However, microbiota assemblages within mosquitoes and the impact of microbiota in environments on mosquito development and survival remain unclear. This study examined microbiota assemblages and the effects of aquatic environment microbiota on the larval development of the Aedes albopictus mosquito, an important dengue virus vector. Life table studies have found that reducing bacterial load in natural aquatic habitats through water filtering and treatment with antibiotics significantly reduced the larva-to-adult emergence rate. This finding was consistent in two types of larval habitats examined-discarded tires and flowerpots, suggesting that bacteria play a crucial role in larval development. Pyrosequencing of the bacterial 16S rRNA gene was used to determine the diversity of bacterial communities in larval habitats and the resulting numbers of mosquitoes under both laboratory and field conditions. The microbiota profiling identified common shared bacteria among samples from different years; further studies are needed to determine whether these bacteria represent a core microbiota. The highest microbiota diversity was found in aquatic habitats, followed by mosquito larvae, and the lowest in adult mosquitoes. Mosquito larvae ingested their bacterial microbiota and nutrients from aquatic habitats of high microbiota diversity. Taken together, the results support the observation that Ae. albopictus larvae are able to utilize diverse bacteria from aquatic habitats and that live bacteria from aquatic habitats play an important role in larval mosquito development and survival. These findings provide new insights into bacteria's role in mosquito larval ecology.

Abstract 576: LDL-Trafficked Small RNAs Promote Atherosclerosis through TLR Signaling in Macrophages

Atherosclerosis is a chronic inflammatory disease, and despite resounding success in lipid management to reduce cardiovascular events, most heart attacks in the US occur in patients with clinically normal LDL-C levels. The next generation of therapies for cardiovascular disease (CVD) will include inflammation-based targets; however, systemic immune suppression has limitations. Thus, the critical barrier for successful targeting of inflammation in CVD is the identification of vascular ligands that drive immune cell activation. Previously, we demonstrated that low-density lipoproteins (LDL) transport microRNAs. Here, we report that LDL traffic a wide-diversity of small non-coding RNAs (sRNA) in circulation, many of which are derived from exogenous species, e.g. bacteria and fungi. Moreover, using high-throughput sRNA sequencing, we found that LDL-sRNA signatures are influenced primarily by environmental microbiota, as opposed to commensal bacteria in the gut microbiome. Using a mouse model of compromised mucosal immunity, we identified a process by which LDL accumulates bacterial sRNAs. Next, we demonstrated that native LDL potently stimulated cytokine release from macrophages through activation of single-stranded RNA (ssRNA)-sensing toll-like receptor (TLR) signaling, which was blunted by partial silencing of ssRNA-sensing TLRs in macrophages. Most importantly, preliminary results in mice suggest that targeting ssRNA-sensing TLRs is a potential strategy to suppress atherosclerosis. Taken together, we put forth a novel paradigm in which, LDL scavenge microbial sRNAs to promote clearance during health, yet serve as TLR-ligands that propagate macrophage inflammation in hypercholesterolemia, which likely contributes to the underlying inflammation in the pathogenesis of CVD.

Anton Chekhov and Robert Koch Cheek to Cheek: A Proteomic Study.

Five different letters and post cards as well as the shirt worn by Anton Chekhov on his death bed, stored in the State Literary-Memorial Museum-Reserve A. P. Chekhov Melikhovo (nearby Moscow), have been analyzed by applying EVA (an ethyl vinyl acetate foil studded with crushed strong anion and cation exchangers and with C8 resins) diskettes to these surfaces. Three different eluates (under acidic and basic conditions and with acetonitrile) were analyzed by high resolution mass spectrometry. The environmental microbiota present on samples and the Mycobacterium tuberculosis strain were described by a meta-proteomics approach. Eight identified M. tuberculosis proteins confirmed the presence of the bacterium and the cause of Chekhov's death, in addition to several sequenced peptides belonging to other bacterial species. The human plasma proteins and human keratins, detected on a tiny blood spot on the shirt, demonstrated the power of the combined approach.

Skin microbiota and allergic symptoms associate with exposure to environmental microbes

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations.

Soil metabarcoding identifies season indicators and differentiators of pig and Agrostis/Festuca spp. decomposition

To gain a better understanding of how environmental microbiota respond to cadaver decomposition, a forensic ecogenomic study was made with soil only control and 4g each of Sus scrofa domesticus and plant litter (Agrostis/Festuca spp.) buried individually in a sandy clay loam (80g) in sealed but perforated triplicate microcosms. The next-generation sequencing (Illumina Miseq) of the soil bacteria (16S rRNA gene) clade revealed seasonal taxomonic shifts at genus-level for the pig and plant litter microcosms compared to the non-burial controls. In particular, numerical abundances of Sphingobacterium (5.9%) and Pedobacter (24.1%) for the pig microcosms, and Rhodanobacter (18.1%) and Shinella (4.6%) for the plant litter microcosms, identified bacterial genera that could be tracked to establish a (seasonal) subsurface postmortem microbial clock. Also, family-level resolution revealed members that were unique to the control, grass and pig soils after 365 days.

The environment as areservoir for antimicrobial resistance : Agrowing problem for public health?

Antimicrobial resistance (AMR) is athreat to public and animal health on the global scale. The origin of the genes associated with resistance has long been unknown. Recently, there is agrowing body of evidence demonstrating that environmental bacteria are resistant to amultitude of antibiotic substances and that this environmental reservoir of AMR is still growing. The analysis of the genomes of bacterial pathogens indicates that they have acquired their resistance profiles by incorporating different genetic elements through horizontal gene transfer. The ancestors of pathogenic bacteria, as well as the origin of resistance determinants, lay most likely in the environmental microbiota. Indeed, there is some evidence that at least some clinically relevant resistance genes have originated in environmental bacterial species. Thus, feasible measures are required to reduce the risks posed by AMR genes and resistant bacteria that occur in the environment. It has been shown that aconcurrence of factors, such as high concentrations of antibiotics or heavy metals used as biocides and high bacterial densities, promote development and spread of antimicrobial resistance. For this purpose, it is essential to restrict the use of antibiotics for the treatment of livestock and humans to medical necessity, as well as to reduce the application of biocides and heavy metals in animal husbandry. Moreover, it is important to further develop sanitary measures at the interface between the environment and clinical settings or livestock farming.

Bioavailability of Antibiotics at Soil-Water Interfaces: A Comparison of Measured Activities and Equilibrium Partitioning Estimates.

There are growing concerns that antibiotic pollution impacts environmental microbiota and facilitates the propagation of antibiotic resistance. However, the prediction or analytical determination of bioavailable concentrations of antibiotics in soil is still subject to great uncertainty. Biological assays are increasingly recognized as valuable complementary tools that allow a more direct determination of the residual antibiotic activity. This study assessed the bioavailability of structurally diverse antibiotics at a soil-water interface applying activity-based analyses in conjunction with equilibrium partitioning (EqP) modeling. The activity against Gram-positive and Gram-negative bacteria of nine antibiotics from different classes was determined in the presence and absence of standard soil (LUFA St. 2.2). The addition of soil affected the activity of different antibiotics to highly varying degrees. Moreover, a highly significant correlation ( p < 0.0001) between the experimentally observed and the EqP-derived log EC50 (half-maximal effective concentration) values was observed. The innovative experimental design of this study provided new insights on the bioavailability of antibiotics at soil-water interfaces. EqP appears to be applicable to a broad range of antibiotics for the purpose of screening-level risk assessment. However, EqP estimates cannot replace soil-specific ecotoxicity testing in higher-tier assessments, since their accuracy is still compromised by a number of factors.

Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water.

Host development influences gut microbial assemblies that may be confounded partly by dietary shifts and the changing environmental microbiota during ontogenesis. However, little is known about microbial colonization by excluding dietary effects and compositional differences in microbiota between the gut and environment at different ontogenetic stages. Herein, a developmental gut microbial experiment under controlled laboratory conditions was conducted with carnivorous southern catfish Silurus meridionalis fed on an identical prey with commensal and abundant microbiota. In this study, we provided a long-term analysis of gut microbiota associated with host age at 8, 18, 35, 65, and 125 day post-fertilization (dpf) and explored microbial relationships among host, food and water environment at 8, 35, and 125 dpf. The results showed that gut microbial diversity in southern catfish tended to increase linearly as host aged. Gut microbiota underwent significant temporal shifts despite similar microbial communities in food and rearing water during the host development and dramatically differed from the environmental microbiota. At the compositional abundance, Tenericutes and Fusobacteria were enriched in the gut and markedly varied with host age, whereas Spirochaetes and Bacteroidetes detected were persistently the most abundant phyla in food and water, respectively. In addition to alterations in individual microbial taxa, the individual differences in gut microbiota were at a lower level at the early stages than at the late stages and in which gut microbiota reached a stable status, suggesting the course of microbial successions. These results indicate that host development fundamentally shapes a key transition in microbial community structure, which is independent of dietary effects. In addition, the dominant taxa residing in the gut do not share their niche habitats with the abundant microbiota in the surrounding environment. It's inferred that complex gut microbiota could not be simple reflections of environmental microbiota. The knowledge enhances the understanding of gut microbial establishment in the developing fish and provides a useful resource for such studies of fish- or egg-associated microbiota in aquaculture.

Half-lives of PAHs and temporal microbiota changes in commonly used urban landscaping materials.

BackgroundPolycyclic aromatic hydrocarbons (PAHs) accumulate in urban soils, and PAH contamination can change soil microbial community composition. Environmental microbiota is associated with human commensal microbiota, immune system and health. Therefore, studies investigating the degradation of PAHs, and the consequences of soil pollution on microbial communities in urban landscaping materials, are crucial.MethodsFour landscaping materials (organic matter 1, 2, 13 and 56%) were contaminated with PAHs commonly found at urban sites (phenanthrene, fluoranthene, pyrene, chrysene and benzo(b)fluoranthene) in PAH concentrations that reflect urban soils in Finland (2.4 µg g -1 soil dry weight). PAHs were analyzed initially and after 2, 4, 8 and 12 weeks by gas chromatography-mass spectrometry. Half-lives of PAHs were determined based on 12-weeks degradation. Bacterial communities were analyzed at 1 and 12 weeks after contamination using Illumina MiSeq 16S rRNA gene metabarcoding.ResultsHalf-lives ranged from 1.5 to 4.4 weeks for PAHs with relatively low molecular weights (phenanthrene, fluoranthene and pyrene) in landscaping materials containing 1–2% organic matter. In contrast, in materials containing 13% and 56% organic matter, the half-lives ranged from 2.5 to 52 weeks. Shorter half-lives of phenanthrene and fluoranthene were thus associated with low organic matter content. The half-life of pyrene was inversely related to the relative abundance of Beta-, Delta- and Gammaproteobacteria, and diversity of Bacteroidetes and Betaprotebacteria. Compounds with higher molecular weights followed compound-specific patterns. Benzo(b)fluoranthene was resistant to degradation and half-life of chrysene was shorter when the relative abundance of Betaproteobacteria was high. Temporal microbiota changes involved increase in the relative abundance of Deltaproteobacteria and decrease in genera Flavobacterium and Rhodanobacter. Exposure to PAHs seems to adjust microbial community composition, particularly within class Beta- and Deltaproteobacteria.ConclusionsIn this study, PAH degradation depended on the organic matter content and bacterial community composition of landscaping materials. Contamination seems to alter bacterial community composition in landscaping materials depending on material type. This alteration includes changes in bacterial phyla associated with human health and immune system. This may open new possibilities for managing urban environments by careful selection of landscaping materials, to benefit health and wellbeing.

Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation

Light-flavour Baijiu is a type of Chinese liquor with a pure and mild flavour produced by traditional spontaneous solid-state fermentation. The flavour of this liquor has been found to vary in the different periods of annual production. To explore the factors affecting flavour, the microbiota of the surrounding environment, starter and fermentation process in different periods were investigated. Results showed that the ester content and acidity of light-flavour Baijiu were significantly lower when annual production was resumed after a summer break. HCA plot of volatile flavour profile and bacterial PCoA results indicated that the differences occurred at later stages, mainly due to different structures of Lactobacillus. Correlation analysis by O2PLS indicated that Lactobacillus positively correlated with esters. Species-level analysis showed that the lack of L. acetotolerans on the surface of the jar might cause a lag in fermentation and lower ester content. Thereafter, L. acetotolerans was revived during fermentation and enriched on the surface of the jar, which promoted ester formation. As important sources of L. acetotolerans, the air and fermentation jars played a critical role during fermentation. Therefore, this systematic study on environmental microbial ecology is valuable for quality control and to explore environmental microbiota functions during spontaneous fermentation.

Symposium review: Lactococcus lactis from nondairy sources: Their genetic and metabolic diversity and potential applications in cheese

The widespread dissemination of species of the lactic acid bacteria (LAB) group in different environments testifies to their extraordinary niche adaptability. Members of the LAB are present on grass and other plant material, in dairy products, on human skin, and in the gastrointestinal and reproductive tracts. The selective pressure imparted by these specific environments is a key driver in the genomic diversity observed between strains of the same species deriving from distinct habitats. Strains that are exploited in the dairy industry for the production of fermented dairy products are often referred to as "domesticated" strains. These strains, which initially may have occupied a nondairy niche, have become specialized for growth in the milk environment. In fact, comparative genome analysis of multiple LAB species and strains has revealed a central trend in LAB evolution: the loss of ancestral genes and metabolic simplification toward adaptation to nutritionally rich environments. In contrast, "environmental" strains, or those from raw milk, plants, and animals, exhibit diverse metabolic capabilities and lifestyle characteristics compared with their domesticated counterparts. Because of the limited number of established dairy strains used in fermented food production today, demand is increasing for novel strains, with concerted efforts to mine the microbiota of natural environments for strains of technological interest. Many studies have concentrated on uncovering the genomic and metabolic potential of these organisms, facilitating comparative genome analysis of strains from diverse environments and providing insight into the natural diversity of the LAB, a group of organisms that is at the core of the dairy industry. The natural biodiversity that exists in these environments may be exploited in dairy fermentations to expand flavor profiles, to produce natural "clean label" ingredients, or to develop safer products.