Sourdough fermentation of bakery products is a well-established and widespread technique to confer an added value to the resulting food. In recent decades, gluten-free raw materials have gained more attention due to the diffusion of food disorders such as coeliac disease, but, at the same time, they present difficult manipulation and scarce technological properties because of the absence of gluten. For this reason, the present work was aimed at selecting starter cultures for sourdough application that are isolated from fermentation of sorghum flour. Three isolates of Lactobacillus fermentum, Weissella cibaria, and Weissella confusa were selected for the following properties: exopolysaccharide synthesis, acidification, CO₂ production, and amylase activity. The investigated phenotypic characteristics were confirmed by genomic analyses, which also highlighted other potentially beneficial features for use in bakery products employment. These strains, together with bakery yeast, were used for bread preparation using sorghum and wheat flour and after 24 h of fermentation the resulting dough was analyzed to assess the improvement of its characteristics. The presence of lactic acid bacteria (LAB) had a great impact on the final dough, and the best preparation, from a rheological point of view, resulted in one made of sorghum and wheat flour with added LAB and bakery yeast, whose resulting characteristics were similar to all wheat flour doughs. The results of this study suggest a potential application of the selected starters in sorghum composite bread and should be validated with data from large-scale pilot tests conducted in industrial bakeries.

A novel Gram-stain-positive, strictly aerobic, short rod-shaped bacterium, designated 2CT, was isolated from freshly packaged microfiltered milk. This strain was able to grow within the NaCl concentration range of 0–5 % (w/v), temperature range of 8–37 °C (optimally at 30 °C) and at pH 6.0–10.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2CT was closely related to species of the genus Microbacterium , with the highest sequence similarity (99.2 %) to Microbacterium lacticum DSM 20427T as well as Microbacterium flavum DSM 18909T (=YM18-098T). The phylogenetic tree based on 16S rRNA genes showed that strain 2CT clustered with M. flavum DSM 18909T. However, the phylogenetic tree based on concatenated 16S rRNA and four housekeeping genes showed that strain 2CT clustered with M. lacticum DSM 20427T. Furthermore, the phylogenomic tree showed that strain 2CT clustered with M. lacticum DSM 20427T and M. flavum DSM 18909T. The major respiratory quinones were MK-10, MK-11 and MK-12. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipid composition of strain 2CT consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified glycolipids and two unidentified lipids. The cell-wall peptidoglycan type was a variant of B1α {Gly} [l-Lys] d-Glu-l-Lys, with the amino acids lysine, glycine, alanine and glutamic acid. The whole-cell sugars consisted of galactose, glucose, ribose and minor amounts of rhamnose. In addition, strain 2CT showed a glycolyl-type cell wall. The genomic DNA G+C content was 69.8mol%, while the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with the closely related Microbacterium species were below the recognized thresholds of 95–96 % ANI and 70 % DDH for species definition. Based on the phenotypic and genotypic data, strain 2CT (=LMG 32277T=CECT 30329T) is considered to represent a new species, for which the name Microbacterium paulum sp. nov. is proposed.

Biogas plants are a widespread renewable energy technology. However, the use of digestate for agronomic purposes has often been a matter of concern. It is controversial whether biogas plants might harbor some pathogenic clostridial species, which represent a biological risk. Moreover, the inhabitance of Clostridium hard-cheese spoiling species in anaerobic digesters can be problematic for hard-cheese manufacturing industries, due to the issue of cheese blowing defects. This study investigated the effect of mesophilic anaerobic digestion processes on the Clostridium consortia distribution over time. Specifically, three lab-scale CSTRs treating agricultural biomass were characterized by considering both the whole microbial community and the cultivable clostridial spores. It is assessed an overall reduction of the Clostridium genus during the anaerobic digestion process. Moreover, it was evidenced a slight, but steady decrease of the cultivable clostridial spores, mainly represented by two pathogenic species, C. perfringens and C. bifermentans, and one hard-cheese spoiling species, C. butyricum. Thus, it is revealed an overall reduction of the clostridial population abundance after the mesophilic anaerobic digestion treatment of agricultural biomass.

Background: The growing population and associated increase in municipal solid waste (MSW) have promoted the use of sustainable waste management strategies. Given its high organic content, MSW can be treated through anaerobic digestion (AD) and aerobic composting (AC) to recover value-added products such as bioenergy and soil amendments. However, MSW is also recognized as a relevant source of antibiotic resistance genes (ARGs), raising concerns about environmental and public health impacts. This study aimed to elucidate the dynamics of ARGs and antibiotic compounds during the treatment of the organic fraction of municipal solid waste (OFMSW) through an integrated AD–AC system. By combining metagenomics and untargeted metabolomics, a comprehensive characterization of shifts in the microbial community, ARGs, and antibiotic compounds throughout the treatment stages was achieved. Shotgun sequencing enabled an in-depth resistome analysis based on metagenome-assembled genomes (MAGs), while untargeted metabolomics revealed the occurrence and transformation of antibiotic compounds across the system. Results: The integrated process resulted in a significant differentiation of microbial communities, resistome, and antibiotic compounds profiles, at different stages of the waste treatment plant. AD samples were mostly dominated by aminoglycoside and lincosamide ARGs, whereas AC samples by macrolide and rifamycin ARGs. Despite differences in drug class dominance, the composting process significantly increased both the ARGs diversity (i.e., digestate: H = 2.6 ± 0.1; mature compost: H = 3.7 ± 0.1) and abundance (i.e., mature compost vs. digestate: log2(FC) = 3.7). Untargeted metabolomics revealed distinct distributions of antibiotics among the six matrices (i.e., pulp, digestate, solid fraction, liquid fraction, fresh compost, and mature compost) suggesting limited degradation or transformation of some classes during treatment. Digestate was enriched in phenazines and trimethoprim derivatives, whereas mature compost mainly included phenicols and sulfonamides. Conclusions: This study provides valuable insights into the fate of antibiotic resistance genes and the persistence of antibiotic compounds in an integrated AD and AC system treating OFMSW. Moreover, it was shown how the integration of -omics techniques as metagenomics and metabolomics can be systematically utilized to detect emerging ARGs and antibiotic compounds dynamics and monitor their ongoing evolution in biological waste treatment plants.

In addition to energy recovery, the anaerobic digestion of agro-industrial byproducts can also produce different high-value-added compounds. Two-stage and single-stage reactors were compared for microbial communities’ selection and long-chain fatty acid (LCFA) accumulation to investigate which microbial genera are most linked to the production of these compounds. The microbial communities present in the two reactors’ configuration in the steady state were characterised by 16S rRNA amplicon sequencing, while LCFAs were extracted and quantified from digestate samples by gas chromatography. The results showed the differentiation of the microbially dominant families in the two setups: Defluviitaleaceae and Clostridiaceae in the acidogenic and methanogenic reactor of the two-stage reaction respectively, while Dysgonomonadaceae in the single-stage set-up. LCFA accumulation was significantly detected only in the acidogenic reactor, with palmitic (2764 mg/kg), linoleic (1795 mg/kg) and stearic (1751 mg/kg) acids as the most abundant. The dominance of Defluviitaleaceae UCG 011, along with the low abundance of the LCFA oxidiser Syntrophomonas spp. in the acidogenic reactor, could be linked to the accumulation of such compounds. Therefore, the different microbial communities shaped by the two reactors’ configuration affected the accumulation of LCFAs, indicating that the two-stage anaerobic digestion of agro-industrial byproducts was more effective than single-stage digestion.