Microbial interactions shape cheese flavour formation.

Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, we studied the roles of microbial interactions in flavour formation in a year-long Cheddar cheese making process, using a commercial starter culture containing Streptococcus thermophilus and Lactococcus strains. By using an experimental strategy whereby certain strains were left out from the starter culture, we show that S. thermophilus has a crucial role in boosting Lactococcus growth and shaping flavour compound profile. Controlled milk fermentations with systematic exclusion of single Lactococcus strains, combined with genomics, genome-scale metabolic modelling, and metatranscriptomics, indicated that S. thermophilus proteolytic activity relieves nitrogen limitation for Lactococcus and boosts de novo nucleotide biosynthesis. While S. thermophilus had large contribution to the flavour profile, Lactococcus cremoris also played a role by limiting diacetyl and acetoin formation, which otherwise results in an off-flavour when in excess. This off-flavour control could be attributed to the metabolic re-routing of citrate by L. cremoris from diacetyl and acetoin towards α-ketoglutarate. Further, closely related Lactococcus lactis strains exhibited different interaction patterns with S. thermophilus, highlighting the significance of strain specificity in cheese making. Our results highlight the crucial roles of competitive and cooperative microbial interactions in shaping cheese flavour profile.

Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN.

Genome-scale metabolic models (GEMs) provide a useful framework for modeling the metabolism of microorganisms. While the applications of GEMs are wide and far reaching, the reconstruction and continuous curation of such models can be perceived as a tedious and time-consuming task. Using RAVEN, a MATLAB-based toolbox designed to facilitate the reconstruction analysis of metabolic networks, this protocol practically demonstrates how researchers can create their own GEMs using a homology-based approach. To provide a complete example, a draft GEM for the industrially relevant yeast Hansenula polymorpha is reconstructed.

Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance.

Microbial communities are composed of cells of varying metabolic capacity, and regularly include auxotrophs that lack essential metabolic pathways. Through analysis of auxotrophs for amino acid biosynthesis pathways in microbiome data derived from >12,000 natural microbial communities obtained as part of the Earth Microbiome Project (EMP), and study of auxotrophic-prototrophic interactions in self-establishing metabolically cooperating yeast communities (SeMeCos), we reveal a metabolically imprinted mechanism that links the presence of auxotrophs to an increase in metabolic interactions and gains in antimicrobial drug tolerance. As a consequence of the metabolic adaptations necessary to uptake specific metabolites, auxotrophs obtain altered metabolic flux distributions, export more metabolites and, in this way, enrich community environments in metabolites. Moreover, increased efflux activities reduce intracellular drug concentrations, allowing cells to grow in the presence of drug levels above minimal inhibitory concentrations. For example, we show that the antifungal action of azoles is greatly diminished in yeast cells that uptake metabolites from a metabolically enriched environment. Our results hence provide a mechanism that explains why cells are more robust to drug exposure when they interact metabolically.

Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends.

Biodegradation is a plausible route toward sustainable management of the millions of tons of plastic waste that have accumulated in terrestrial and marine environments. However, the global diversity of plastic-degrading enzymes remains poorly understood. Taking advantage of global environmental DNA sampling projects, here we constructed hidden Markov models from experimentally verified enzymes and mined ocean and soil metagenomes to assess the global potential of microorganisms to degrade plastics. By controlling for false positives using gut microbiome data, we compiled a catalogue of over 30,000 nonredundant enzyme homologues with the potential to degrade 10 different plastic types. While differences between the ocean and soil microbiomes likely reflect the base compositions of these environments, we find that ocean enzyme abundance increases with depth as a response to plastic pollution and not merely taxonomic composition. By obtaining further pollution measurements, we observed that the abundance of the uncovered enzymes in both ocean and soil habitats significantly correlates with marine and country-specific plastic pollution trends. Our study thus uncovers the earth microbiome's potential to degrade plastics, providing evidence of a measurable effect of plastic pollution on the global microbial ecology as well as a useful resource for further applied research. IMPORTANCE Utilization of synthetic biology approaches to enhance current plastic degradation processes is of crucial importance, as natural plastic degradation processes are very slow. For instance, the predicted lifetime of a polyethylene terephthalate (PET) bottle under ambient conditions ranges from 16 to 48 years. Moreover, although there is still unexplored diversity in microbial communities, synergistic degradation of plastics by microorganisms holds great potential to revolutionize the management of global plastic waste. To this end, the methods and data on novel plastic-degrading enzymes presented here can help researchers by (i) providing further information about the taxonomic diversity of such enzymes as well as understanding of the mechanisms and steps involved in the biological breakdown of plastics, (ii) pointing toward the areas with increased availability of novel enzymes, and (iii) giving a basis for further application in industrial plastic waste biodegradation. Importantly, our findings provide evidence of a measurable effect of plastic pollution on the global microbial ecology.

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes.

Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses.

Anormalidades fetais diagnosticadas ecograficamente e que têm resoluçåo espontânea intra-útero ou no período neonatal / Ultrasound diagnostic of fetal anomalies with intra-utero or neonatal spontaneous resolution

Apresenta-se a evoluçåo de 12 casos de anomalias fetais que apresentaram resoluçåo espontânea intra-útero ou no período neonatal. As lesöes fetais foram cisto de plexo coróideo (4 casos), higroma cístico (1 caso), ascite (1 caso), arritmias cardíacas (6 casos). Discute-se a natureza e evoluçåo das lesöes fetais reversíveis