Microbes produce an array of secondary metabolites that perform diverse functions from communication to defense. These metabolites have been used to benefit human health and sustainability. In their analysis of the Genomes from Earth's Microbiomes (GEM) catalog, Nayfach and co-authors observed that, whereas genes coding for certain classes of secondary metabolites are limited or enriched in certain microbial taxa, "specific chemistry is not limited or amplified by the environment, and that most classes of secondary metabolites can be found nearly anywhere". Although metagenome mining is a powerful way to annotate biosynthetic gene clusters (BCGs), chemical evidence is required to confirm the presence of metabolites and comprehensively address this fundamental hypothesis, as metagenomic data only identify metabolic potential. To describe the Earth's metabolome, we use an integrated omics approach: the direct survey of metabolites associated with microbial communities spanning diverse environments using untargeted metabolomics coupled with metagenome analysis. We show, in contrast to Nayfach and co-authors, that the presence of certain classes of secondary metabolites can be limited or amplified by the environment. Importantly, our data indicate that considering the relative abundances of secondary metabolites (i.e., rather than only presence/absence) strengthens differences in metabolite profiles across environments, and that their richness and composition in any given sample do not directly reflect those of co-occurring microbial communities, but rather vary with the environment.

1Background 2The existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but 3 in human populations efforts to identify microbial biomarkers have been limited due to problems stratifying participants 4 within the broad phenotype of ASD and a lack of appropriately matched controls. To overcome these limitations and 5 investigate the relationship between ASD and the gut microbiome, we ran a crowdsourced study of families 2-7 year old 6 sibling pairs, where one child of the pair had a diagnosis of ASD and the other child did not. 7 Methods 8Parents of age-matched sibling pairs electronically consented and completed study procedures via a secure web portal 9 (microbiome.stanford.edu). Parents collected stool samples from each child, responded to behavioral questionnaires about 10 the ASD child's typical behavior, and whenever possible provided a home video of their ASD child's natural social 11 behavior. We performed DNA extraction and 16S rRNA amplicon sequencing on 117 stool samples (60 ASD and 57 NT) 12 that met all study design eligibility criteria,. Using DADA2, Exact Sequence Variants (ESVs) were identified as 13 taxonomic units, and three statistical tests were performed on ESV abundance counts: (1) permutation test to determine 14 differences between sibling pairs, (2) differential abundance test using a zero-inflated gaussian mixture model to account 15 for the sparse abundance matrix, and (3) differential abundance test after modeling under a negative binomial distribution. 16The potential functional gene abundance for each sample was also inferred from the 16S rRNA data, providing KEGG 17 Ortholog (KO) , which were analyzed for differential abundance. 18 Results 19In total, 21 ESVs had significantly differentially proportions in stool of children with ASD and their neurotypical siblings. 20Of these 21 ESVs, 11 were enriched in neurotypical children and ten were enriched in children with ASD. ESVs enriched 21 in the ASD cohort were predominantly associated with Ruminococcaceae and Bacteroidaceae; while those enriched in 22 controls were more diverse including taxa associated with Bifidobacterium, Porphyromonas, Slackia, Desulfovibrio, 23 Acinetobacter johnsonii, and Lachnospiraceae. Exact Variant Analysis suggested that Lachnospiraceae was specific to the 24 control cohort, while Ruminococcaceae, Tissierellaceae and Bacteroidaceae were significantly enriched in children with 25 ASD. Metabolic gene predictions determined that while both cohorts harbor the butyrogenic pathway, the ASD cohort 26 was more likely to use the 4-aminobutanoate (4Ab) pathway, while the control cohort was more likely to use the pyruvate 27 pathway. The 4Ab pathway releases harmful by-products like ammonia and can shunt glutamate, affecting its availability 28 as an excitatory neurotransmitter. Finally, we observed differences in the carbohydrate uptake capabilities of various 29ESVs identified between the two cohorts. 30 31 3 1 INTRODUCTION 2Autism spectrum disorder (ASD) is ...

A swine model was developed to investigate the efficacy of percutaneous venous catheters with anti-microbial coatings. The catheters used in the study consisted of silver-coated and uncoated catheters, both designed for percutaneous venous access. Five commercial pigs were each implanted with three venous catheters and followed for a period of 90 days. Two of the three catheters were coated and one was uncoated. To evaluate the percutaneous aspects of the catheters in the model, two venous access catheters were implanted percutaneously, parallel to the dorsal midline. These catheters were just caudal to the region that is dorsal to the scapula in each animal. In each case, the catheter to the left of the dorsal midline was silver-coated while the catheter to the right of the dorsal midline was uncoated. A silver-coated catheter was also implanted in the left external jugular vein of each animal and buried subcutaneously in order to evaluate the elution of the coating through the body under venous contact. Over the 90 day period, the concentration of silver in the blood rose to a mean peak level of 23.2 ppb following implantation of the catheters and then decreased after the second post-surgery week. The histological evaluation and macroscopic inspection at necropsy revealed minimal tissue response to both coated and uncoated materials. Data on bacterial growth indicated that bacteria were present at the terminal subcutaneous end of two of the uncoated percutaneous catheters. Based upon serum silver levels, exudate formation, histological examination, and bacterial growth information, the swine model was deemed to be suitable for testing the efficacy of catheters containing anti-microbial coatings.

Previous studies demonstrate an exchange of bacteria between hospital room surfaces and patients, and a reduction in survival of microorganisms in dust inside buildings from sunlight exposure. While the transmission of microorganisms between humans and their local environment is a continuous exchange which generally does not raise cause for alarm, in a hospital setting with immunocompromised patients, these building-source microbial reservoirs may pose a risk. Window glass is often neglected during hospital disinfection protocols, and the microbial communities found there have not previously been examined. This pilot study examined whether living bacterial communities, and specifically the pathogens Methicillin-resistant Staphylococcus aureus (MRSA) and Clostridioides difficile (C. difficile), were present on window components of exterior-facing windows inside patient rooms, and whether relative light exposure (direct or indirect) impacts bacterial communities on those hospital surfaces. Environmental samples were collected from 30 patient rooms from a single ward at Oregon Health and Science University (OHSU) in Portland, Oregon, USA. Sampling locations within each room included the window glass surface, both sides of the window curtain, two surfaces of the window frame, and the air return grille. Viable bacterial abundances were quantified using qPCR, and community composition was assessed using Illumina MiSeq sequencing of the 16S rRNA gene V3/V4 region. Viable bacteria occupied all sampled locations, but was not associated with a specific hospital surface or relative sunlight exposure. Bacterial communities were similar between window glass and the rest of the room, but had significantly lower Shannon Diversity, theorized to be related to low nutrient density and resistance to bacterial attachment of glass compared to other surface materials. Rooms with windows that were facing west demonstrated a higher abundance of viable bacteria than those facing other directions, potentially because at the time of sampling (morning)

BackgroundAgricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear.MethodsWe performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities.ResultsPhysicochemical properties including TN, TP, NO3--N, and NO2--N were correlated with microbial compositional differences in water samples. Likewise, in sediment samples, Sed-OM and Sed-TN correlated with microbial diversity. Oxytetracycline and tetracycline concentration described the majority of the variance in taxonomic and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Finally, the structure of microbial co-associations was influenced by the eutrophication and antibiotic pollution.ConclusionThese analyses of the composition and structure of water and sediment microbial communities in anthropologically-impacted lakes are imperative for effective environmental pollution monitoring. Likewise, the exploration of the associations between environmental variables (e.g. physicochemical properties, and antibiotics) and community structure is important in the assessment of lake water quality and its ability to sustain agriculture. These results show agricultural practices can negatively influence not only the physicochemical properties, but also the biodiversity of microbial communities associated with the Honghu lake ecosystem. And these results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu lake.