Chemical-physical parameters and microbial community changes induced by electrodes polarization inhibit PCB dechlorination in a marine sediment.

Microbial reductive dechlorination of organohalogenated pollutants is often limited by the scarcity of electron donors, that can be overcome with microbial electrochemical technologies (METs). In this study, polarized electrodes buried in marine sediment microcosms were investigated to stimulate PCB reductive dechlorination under potentiostatic (-0.7 V vs Ag/AgCl) and galvanostatic conditions (0.025 mA·cm-2-0.05 mA·cm-2), using graphite rod as cathode and iron plate as sacrificial anode. A single circuit and a novel two antiparallel circuits configuration (2AP) were investigated. Single circuit polarization impacted the sediment pH and redox potential (ORP) proportionally to the intensity of the electrical input and inhibited PCB reductive dechlorination. The effects on the sediment's pH and ORP, along with the inhibition of PCB reductive dechlorination, were mitigated in the 2AP system. Electrodes polarization stimulated sulfate-reduction and promoted the enrichment of bacterial clades potentially involved in sulfate-reduction as well as in sulfur oxidation. This suggested the electrons provided were consumed by competitors of organohalide respiring bacteria and specifically sequestered by sulfur cycling, which may represent the main factor limiting the applicability of METs for stimulating PCB reductive dechlorination in marine sediments.

Application of multi-omic features clustering and pathway enrichment to clarify the impact of vitamin B2 supplementation on broiler caeca microbiome.

Background: The results of omic methodologies are often reported as separate datasets. In this study we applied for the first time multi-omic features clustering and pathway enrichment to clarify the biological impact of vitamin B2 supplementation on broiler caeca microbiome. Methods: The caeca contents of broilers fed +50 and +100 mg/kg vitamin B2 were analyzed by shotgun metagenomic and metabolomic. Latent variables extracted from NMR spectra, as well as taxonomic and functional features profiled from metagenomes, were integrated to characterize the effect of vitamin B2 in modulating caeca microbiome. A pathway-based network was obtained by mapping the observed input genes and compounds, highlighting connected strands of metabolic ways through pathway-enrichment analysis. Results: At day 14, the taxonomic, functional and metabolomic features in the caeca of tested broilers showed some degree of separation between control and treated groups, becoming fully clear at 28 days and persisting up to 42 days. In the caeca of birds belonging to the control group Alistipes spp. was the signature species, while the signature species in the caeca of broilers fed +50 and +100 mg/kg vitamin B2 were Bacteroides fragilis and Lactobacillus crispatus, Lactobacillus reuteri, Ruminococcus torques, Subdoligranum spp., respectively. The pathway enrichment analysis highlighted that the specific biochemical pathways enhanced by the supplementations of vitamin B2 were N-Formyl-L-aspartate amidohydrolase, producing Aspartate and Formate; L-Alanine:2-oxoglutarate amino transferase, supporting the conversion of L-Alanine and 2-Oxoglutarate in Pyruvate and L-Glutamate; 1D-myo-inositol 1/4 phosphate phosphohydrolase, converting Inositol 1/4-phosphate and water in myo-Inositol and Orthophosphate. The results of this study demonstrated that the caeca of birds fed +50 and + 100 mg/kg were those characterized by taxonomic groups more beneficial to the host and with a higher concentration of myo-inositol, formic acid, amino acids and pyruvate involved in glycolysis and amino acid biosynthesis. Conclusion: In this study we demonstrated how to perform multi-omic features integration to describe the biochemical mechanisms enhanced by the supplementation of different concentrations of vitamin B2 in the poultry diet. The relationship between vitamin B2 supplementation and myo-inositol production was highlighted in our study for the first time.

Site-specific response of sediment microbial community to supplementation of polyhydroxyalkanoates as biostimulants for PCB reductive dechlorination.

The use of biodegradable plastics is constantly raising, increasing the likeliness for these polymers to end up in the environment. Environmental applications foreseeing the intentional release of biodegradable plastics have been also recently proposed, e.g., for polyhydroxyalkanoates (PHAs) acting as slow hydrogen releasing compounds to stimulate microbial reductive dehalogenation processes. However, the effects of their release into the environment on the ecosystems still need to be thoroughly explored. In this work, the use of PHAs to enhance the microbial reductive dechlorination of polychlorobiphenyls (PCBs) and their impact on the metabolic and compositional features of the resident microbial community have been investigated in laboratory microcosms of a polluted marine sediment from Mar Piccolo (Taranto, Italy), and compared with recent findings on a different contaminated marine sediment from Pialassa della Baiona (Ravenna, Italy). A decreased biostimulation efficiency of PHAs on PCBs reductive dechlorination was observed in the sediment from Mar Piccolo, with respect to the sediment from Pialassa della Baiona, suggesting that the sediments' physical-chemical characteristics and/or the biodiversity and composition of its microbial community might play a key role in determining the outcome of this biostimulation strategy. Regardless of the sediment origin, PHAs were found to have a specific and pervasive effect on the sediment microbial community, reducing its biodiversity, defining a newly arranged microbial core of primary degraders and consequently affecting, in a site-specific way, the abundance of subdominant bacteria, possibly cross-feeders. Such potential to dramatically change the structure of autochthonous microbial communities should be carefully considered, since it might have secondary effects, e.g., on the natural biogeochemical cycles.

Effect of polyhydroxyalkanoates on the microbial reductive dechlorination of polychlorinated biphenyls and competing anaerobic respirations in a marine microbial culture.

The effect of polyhydroxyalkanoates (PHAs) with different composition on the reductive dechlorination activity of a polychlorinated biphenyls (PCBs) dechlorinating marine microbial community and on the activity of sulfate-reducing (SRB) and methanogenic bacteria (MB), were investigated in marine sediment microcosms and compared with the main monomer, 3-hydroxybutyric acid (3HB). Despite PHAs were fermented more slowly than 3HB, all electron donors stimulated constantly sulfate-reduction, methanogenesis and, only transiently, PCB reductive dechlorination. No relevant differences were observed with different compositions of PHAs. According to electron balances, the majority of the supplied electrons (50 %) were consumed by SRB and to less extent by MB (9-31 %), while a small percentage (0.01 %) was delivered to OHRB. In the studied conditions PHAs were confirmed as potential slow­hydrogen releasing compounds in marine environment but their fermentation rate was sufficiently high to mainly stimulate the competitors of organohalide respring bacteria for electron donors.

Exploration of Tools for the Interpretation of Human Non-Coding Variants.

The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challenging issues in WGS analysis regards the interpretation of annotated variants. This review focuses on tools suitable for the functional annotation of variants falling into non-coding regions. It couples the description of non-coding genomic areas with the results and performance of existing tools for a functional interpretation of the effect of variants in these regions. Tools were tested in a controlled genomic scenario, representing the ground-truth and allowing us to determine software performance.

Bacterial colonization dynamics of different microplastic types in an anoxic salt marsh sediment and impact of adsorbed polychlorinated biphenyls on the plastisphere.

Plastic debris dispersed into the environment provide a substrate for microbial colonization, constituting a new human-made ecosystem called "plastisphere", and altering the microbial species distribution in aquatic, coastal and benthic ecosystems. The study aims at exploring the interaction among microplastics (MPs) made of different polymers, a persistent organic contaminant (polychlorinated biphenyls, PCBs), and the environmental microbial communities, in an anoxic marine sediment. Plastic pellets were incubated in the field in a salt marsh anoxic sediment, to observe the stages of plastisphere formation, by quantitative PCR and 16S rRNA gene sequencing, and PCB dechlorination activity on the MPs surface. Microbes from the sediment rapidly colonized the different microplastics types, with PVC recruiting a peculiar community enriched in sulfate-reducing bacteria. The composition of the plastisphere varied along the 1-year incubation possibly in response either to warmer temperatures in spring-summer or to microhabitat's changes due to the progressive plastic surface weathering. Even if PCB contaminated MPs were able to recruit potentially dehalogenating taxa, actual dechlorination was not detectable after 1 year. This suggests that the concentration of potentially dehalorespiring bacteria in the natural environment could be too low for the onset of the dechlorination process on MP-sorbed contaminants. Our study, which is among very few available longitudinally exploring the plastisphere composition in an anoxic sediment context, is the first exploring the fate and possible biodegradation of persistent organic pollutants sorbed on MPs reaching the seafloor.

A Pilot Study on Donor Human Milk Microbiota: A Comparison with Preterm Human Milk Microbiota and the Effect of Pasteurization.

Human milk (HM) is the best feeding option for preterm infants; however, when mother's own milk (MOM) is not available, pasteurized donor human milk (DHM) is the best alternative. In this study, we profiled DHM microbiota (19 samples) using 16S rRNA amplicon sequencing and compared its compositional features with the MOM microbiota (14 samples) from mothers who delivered prematurely (PT-MOM). As a secondary study aim, we assessed the specific effect of pasteurization on the characteristics of the DHM microbiota. DHM showed significantly higher alpha diversity and significant segregation from PT-MOM. Compositionally, the PT-MOM microbiota had a significantly higher proportion of Staphylococcus than DHM, with Streptococcus tending to be and Pseudomonas being significantly overrepresented in DHM compared with the PT-MOM samples. Furthermore, pasteurization affected the HM microbiota structure, with a trend towards greater biodiversity and some compositional differences following pasteurization. This pilot study provided further evidence on the HM microbial ecosystem, demonstrating that the DHM microbiota differs from the PT-MOM microbiota, possibly due to inherent differences between HM donors and mothers delivering prematurely, and that pasteurization per se impacts the HM microbiota. Knowledge about HM microbiota needs to be acquired by investigating the effect of DHM processing to develop strategies aimed at improving DHM quality while guaranteeing its microbiological safety.

Fecal Microbiota Monitoring in Elite Soccer Players Along the 2019-2020 Competitive Season.

Physical exercise affects the human gut microbiota, which in turn influences athletes' performance. The current understanding of how the microbiota of professional athletes changes along with different phases of training is sparse. We aim to characterize the fecal microbiota in elite soccer players along with different phases of a competitive season using 16 S rRNA gene sequencing. Fecal samples were collected after the summer off-season period, the pre-season retreat, the first half of the competitive season, and the 8 weeks of COVID-19 lockdown that interrupted the season 2019-2020. According to our results, the gut microbiota of professional athletes changes along with the phases of the season, characterized by different training, diet, nutritional surveillance, and environment sharing. Pre-season retreat, during which nutritional surveillance and exercise intensity were at their peak, caused a decrease in bacterial groups related to unhealthy lifestyle and an increase in health-promoting symbionts. The competitive season and forced interruption affected other features of the athletes' microbiota, i.e., bacterial groups that respond to dietary fiber load and stress levels. Our longitudinal study, focusing on one of the most followed sports worldwide, provides baseline data for future comparisons and microbiome-targeting interventions aimed at developing personalized training and nutrition plans for performance maximization.

Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient.

Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.

Early-life gut microbiota and neurodevelopment in preterm infants: any role for Bifidobacterium?

Despite the well-recognized importance of proper gut microbiota assembly for the child's future health, the connections between the early-life gut microbiota and neurocognitive development in humans have not been thoroughly explored so far. In this pilot observational study, we aimed to unveil the relation between dynamic succession of the gut microbiota in very low birth weight infants during the first month of life and their neurodevelopment, assessed at 24-month corrected age. According to our data, the early-life gut microbiota of preterm infants with normal vs. impaired neurodevelopment followed distinct temporal trajectories with peculiar compositional rearrangements. In this context, early Bifidobacterium deficiency appears to be a negative biomarker of adverse neurological outcomes. CONCLUSION: Our data might pave the way for future in-depth studies focusing on the potential impact of bifidobacteria or specific microbiota patterns on neonatal neurodevelopment and lay the foundation for microbiome-based clinical practices to modulate altered profiles and improve long-term health. WHAT IS KNOWN: • Preterm infants are at increased risk for adverse neurological outcomes and gut microbiota dysbiosis. • The gut microbiota and the nervous system share critical developmental windows in early life. WHAT IS NEW: • The absence of Bifidobacterium at 30 days of life in preterm infants is associated with neurodevelopmental impairment in early childhood. • The administration of Bifidobacterium strains could promote optimal neurocognitive development in fragile infants.

The Gut Microbiota of an Individual Varies With Intercontinental Four-Month Stay Between Italy and Nigeria: A Pilot Study.

Despite well-established knowledge of the role of diet and the geographic effect on the gut microbiota of human populations, the temporal dynamics of the individual microbiota profile across changes associated with intercontinental short residence are still far from being understood. This pilot study sought to provide insights into the trajectory of the gut microbiota of an individual during a two-month stay in Italy and a subsequent two-month stay in Nigeria, by 16S rRNA gene sequencing and inferred metagenomics. The gut microbiota underwent massive but temporary changes, both taxonomically and based on predicted functionality. The faecal microbiota associated with the short stay in Italy progressively lost diversity and showed a dominance of Firmicutes, while after returning to Nigeria, the microbial community quickly regained the typical profile, in terms of biodiversity and bacterial signatures of traditional lifestyle, i.e., Prevotella and Treponema. Predicted pathways involved in glycolysis, fermentation and N-acetylneuraminate degradation were enriched during the subsequent two-month stay in Nigeria, whereas pathways associated with amino acid and peptidoglycan synthesis and maturation became over-represented during short stay in Italy. Our findings stress the plasticity of the individual gut microbiota even during a short-term travel, with loss/gain of taxonomic and functional features that mirror those of the gut microbiota of indigenous people dwelling therein.

Searching for New Microbiome-Targeted Therapeutics through a Drug Repurposing Approach.

Commonly used non-antibiotic drugs have been associated with changes in gut microbiome composition, paving the way for the possibility of repurposing FDA-approved molecules as next-generation microbiome therapeutics. Herein, we developed and validated an ex vivo high-throughput screening platform─the mini gut model─to underpin human gut microbiome response to molecular modulators. Ten FDA-approved compounds, selected based on maximum structural diversity of molecular fingerprints, were screened against the gut microbiome of five healthy subjects to characterize the ability of human-targeted drugs to modulate the human gut microbiome network. Three compounds, THIP hydrochloride, methenamine, and mesna, have shown promise as novel gut microbiome therapeutics in light of their capability of promoting health-associated features of the gut microbiome. Our findings provide a resource for future research on drug-microbiome interactions and lay the foundation for a new era of more precise gut microbiome modulation through drug repurposing, aimed at targeting specific dysbiotic events.

The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs.

In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600-3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response.

Early modifications of the gut microbiome in children with hepatic sinusoidal obstruction syndrome after hematopoietic stem cell transplantation.

Hepatic sinusoidal obstruction syndrome (SOS/VOD) represents a dramatic complication of hematopoietic stem cell transplantation (HSCT), particularly in children. Recent evidence has suggested a role for the gut microbiome (GM) in the context of HSCT and its related complications, but no data are available on the relationship between GM and SOS/VOD. Here, we conducted a retrospective case-control study in allo-HSCT pediatric patients developing or not SOS/VOD and profiled their GM over time, from before the transplant up to 72 days after. A rich and diverse GM before HSCT was found to be associated with a reduced likelihood of developing SOS/VOD. Furthermore, prior to transplant, patients not developing SOS/VOD showed an enrichment in some typically health-associated commensals, such as Bacteroides, Ruminococcaceae and Lachnospiraceae. Their levels remained overall higher until post-transplant. This high-diversity configuration resembles that described in other studies for other HSCT-related complications, including graft-versus-host disease, potentially representing a common protective GM feature against HSCT complications.

G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data.

Deep learning methodologies have revolutionized prediction in many fields and show the potential to do the same in microbial metagenomics. However, deep learning is still unexplored in the field of microbiology, with only a few software designed to work with microbiome data. Within the meta-community theory, we foresee new perspectives for the development and application of deep learning algorithms in the field of the human microbiome. In this context, we developed G2S, a bioinformatic tool for taxonomic prediction of the human fecal microbiome directly from the oral microbiome data of the same individual. The tool uses a deep convolutional neural network trained on paired oral and fecal samples from populations across the globe, which allows inferring the stool microbiome at the family level more accurately than other available approaches. The tool can be used in retrospective studies, where fecal sampling was not performed, and especially in the field of paleomicrobiology, as a unique opportunity to recover data related to ancient gut microbiome configurations. G2S was validated on already characterized oral and fecal sample pairs, and then applied to ancient microbiome data from dental calculi, to derive putative intestinal components in medieval subjects.

Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages.

Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.

Elevated gut microbiome abundance of Christensenellaceae, Porphyromonadaceae and Rikenellaceae is associated with reduced visceral adipose tissue and healthier metabolic profile in Italian elderly.

Aging is accompanied by physiological changes affecting body composition and functionality, including accumulation of fat mass at the expense of muscle mass, with effects upon morbidity and quality of life. The gut microbiome has recently emerged as a key environmental modifier of human health that can modulate healthy aging and possibly longevity. However, its associations with adiposity in old age are still poorly understood. Here we profiled the gut microbiota in a well-characterized cohort of 201 Italian elderly subjects from the NU-AGE study, by 16S rRNA amplicon sequencing. We then tested for association with body composition from dual-energy X-ray absorptiometry (DXA), with a focus on visceral and subcutaneous adipose tissue. Dietary patterns, serum metabolome and other health-related parameters were also assessed. This study identified distinct compositional structures of the elderly gut microbiota associated with DXA parameters, diet, metabolic profiles and cardio-metabolic risk factors.

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.