The role of early life factors and green living environment in the development of gut microbiota in infancy: Population-based cohort study.

Objective: Early life microbial exposure influences the composition of gut microbiota. We investigated how early life factors, and the green living environment around infants' homes, influence the development of gut microbiota during infancy by utilizing data from the Steps to Healthy Development follow-up study (the STEPS study).

Methods: The gut microbiota was analyzed at early (∼3 months, n = 959), and late infancy (∼13 months, n = 984) using 16S rRNA amplicon sequencing, and combined with residential green environment, measured as (1) Normalized Difference Vegetation Index, (2) Vegetation Cover Diversity, and (3) Naturalness Index within a 750 m radius.

Complete genome sequences of 30 bacterial species from a synthetic community.

We present complete genome sequences from 30 bacterial species that can be used to construct defined synthetic communities that stably form in the laboratory under controlled conditions.

Foundation species stabilize an alternative eutrophic state in nutrient-disturbed ponds via selection on microbial community.

Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: (a freshwater mussel) and (a macrophyte).

Molecular Characterisation of Faecal Bacterial Assemblages Among Four Species of Syntopic Odonates.

Factors such as host species, phylogeny, diet, and both timing and location of sampling are thought to influence the composition of gut-associated bacteria in insects. In this study, we compared the faecal-associated bacterial taxa for three Coenagrion and one Enallagma damselfly species. We expected high overlap in representation of bacterial taxa due to the shared ecology and diet of these species.

Portable BLAST-like algorithm library and its implementations for command line, Python, and R.

Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches across nucleotide and amino acid sequences, leading to diverse applications such as protein domain identification, orthology searches, and phylogenetic annotation. Most BLAST implementations are command line tools which produce output as comma-separated values files.

Glyphosate and a glyphosate-based herbicide affect bumblebee gut microbiota.

Pollinator decline is one of the gravest challenges facing the world today, and the overuse of pesticides may be among its causes. Here, we studied whether glyphosate, the world's most widely used pesticide, affects the bumblebee gut microbiota. We exposed the bumblebee diet to glyphosate and a glyphosate-based herbicide and quantified the microbiota community shifts using 16S rRNA gene sequencing.

Prider: multiplexed primer design using linearly scaling approximation of set coverage.

Background: Designing oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing multiplexed primers and probes to complex, heterogeneous DNA data sets, an optimization problem can arise where the smallest number of oligonucleotides covering the largest diversity of the input dataset needs to be identified. Tools that provide this optimization in an efficient manner for large input data are currently lacking.

Quantitative online survey of self-perceived knowledge and knowledge gaps of medicines research and development among Finnish general public.

Objectives: This study explored self-reported knowledge and interest to learn more about medicines research, development and health technology assessment among Finnish general public. It also aimed to define possible knowledge gaps and needs for public education regarding these topics.

Design: Online survey with 503 participants.

Wastewater constituents impact biofilm microbial community in receiving streams.

Microbial life in natural biofilms is dominated by prokaryotes and microscopic eukaryotes living in dense association. In stream ecosystems, microbial biofilms influence primary production, elemental cycles, food web interactions as well as water quality. Understanding how biofilm communities respond to anthropogenic impacts, such as wastewater treatment plant (WWTP) effluent, is important given the key role of biofilms in stream ecosystem function.

Characteristics and outcomes of the Finnish ectopic ACTH syndrome cohort.

Purpose: Ectopic ACTH syndrome (EAS) is rare. We established a national cohort to increase awareness and address unmet needs.

Methods: The Finnish national EAS cohort includes 60 patients diagnosed in 1997-2016.

Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewater.

Multiple anthropogenic drivers are changing ecosystems globally, with a disproportionate and intensifying impact on freshwater habitats. A major impact of urbanization are inputs from wastewater treatment plants (WWTPs). Initially designed to reduce eutrophication and improve water quality, WWTPs increasingly release a multitude of micropollutants (MPs; i.

Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates.

Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously.

Discovery of Membrane-Bound Pyrophosphatase Inhibitors Derived from an Isoxazole Fragment.

Membrane-bound pyrophosphatases (mPPases) regulate energy homeostasis in pathogenic protozoan parasites and lack human homologues, which makes them promising targets in . malaria. Yet only few nonphosphorus inhibitors have been reported so far.

The evolution of competitive ability for essential resources.

Competition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species' minimum resource requirements, their *s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered-to what extent are species' competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposed for approximately 285 generations to seven environments in chemostats that differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress.

Author Correction: Proteome evolution under non-substitutable resource limitation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Uncovering microbial inter-domain interactions in complex communities.

Interactions between unicellular eukaryotes and bacteria are difficult to characterize in the environment owing to their large number and inherently microscopic scale. Although particular co-occurrences can be recovered through targeted approaches, e.g.

Occurrence of sul and tet(M) genes in bacterial community in Japanese marine aquaculture environment throughout the year: Profile comparison with Taiwanese and Finnish aquaculture waters.

The use of antibiotics in aquaculture causes selection pressure for antibiotic-resistant bacteria (ARB). Antibiotic resistance genes (ARGs) may persist in ARB and the environment for long time even after stopping drug administration. Here we show monthly differences in the occurrences of genes conferring resistance to sulfonamides (i.

Proteome evolution under non-substitutable resource limitation.

Resource limitation is a major driver of the ecological and evolutionary dynamics of organisms. Short-term responses to resource limitation include plastic changes in molecular phenotypes including protein expression. Yet little is known about the evolution of the molecular phenotype under longer-term resource limitation.

Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes.

Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the effects of low concentrations of antibiotics on multispecies microbial communities. Here, we address this question by investigating the effects of low antibiotic concentration on community composition and horizontal transfer of an antibiotic resistance plasmid in a 62-strain bacterial community in response to manipulation of the spatial environment and presence of predation.

Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution.

Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems.

Archaea are prominent members of the prokaryotic communities colonizing common forest mushrooms.

In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study.

Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent.

Wastewater treatment plants (WWTPs) collect wastewater from various sources for a multi-step treatment process. By mixing a large variety of bacteria and promoting their proximity, WWTPs constitute potential hotspots for the emergence of antibiotic resistant bacteria. Concerns have been expressed regarding the potential of WWTPs to spread antibiotic resistance genes (ARGs) from environmental reservoirs to human pathogens.

A nationwide study on parathyroid carcinoma.

Background: Parathyroid carcinoma (PC) is rare and diagnostically challenging. Reported outcomes are rather poor and the incidence might be increasing.

Material And Methods: We performed a nationwide study on all cases (n= 32) diagnosed in 2000-2011 in Finland, and compared clinical and histopathological characteristics and outcome to atypical parathyroid (APA; n= 28) and parathyroid adenomas (PA; n= 72).

Biliary Anomalies in Patients With HNF1B Diabetes.

Context: The clinical spectrum of organogenetic anomalies associated with HNF1B mutations is heterogeneous. Besides cystic kidney disease, diabetes, and various other manifestations, odd cases of mainly neonatal and posttransplantation cholestasis have been described. The biliary phenotype is incompletely defined.