Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization

Development of a flow-cell bioreactor for immobilized sulfidogenic sludge characterization using electrochemical H2S microsensors

The sulfate-reduction process plays a crucial role in the biological valorization of SOx gases. However, a complete understanding of the sulfidogenic process in bioreactors is limited by the lack of technologies for characterizing the sulfate-reducing activity of immobilized biomass. In this work, we propose a flow-cell bioreactor (FCB) for characterizing sulfate-reducing biomass using H2S microsensors to monitor H2S production in real-time within a biofilm. To replace natural immobilization through extracellular polymeric substance production, sulfidogenic sludge was artificially immobilized using polymers. Physical and sulfate-reducing activity studies were performed to select a polymer-biomass matrix that maintained sulfate-reducing activity of biomass while providing strong microbial retention and mechanical strength. Several operational conditions of the sulfidogenic reactor allowed to obtain a H2S profiles under different inlet sulfate loads and, additionally, 3D mapping was assessed in order to perform a hydraulic characterization. Besides, the effects of artificial immobilization on biodiversity were investigated through the characterization of microbial communities. This study demonstrated the appropriateness of immobilized-biomass for characterization of sulfidogenic biomass in FCB using H2S electrochemical microsensors, and beneficial microbiological communities shifts as well as enrichment of sulfate-reducing bacteria have been confirmed.

Mass transfer vectors for nitric oxide removal through biological treatments

The reduction of nitric oxide (NO) emissions to atmosphere has been recently addressed using biological technologies. However, NO removal through bioprocesses is quite challenging due to the low solubility of NO in water. Therefore, the abatement of NO emissions might be improved by adding a chelating agent or a mass transfer vector (MTV) to increase the solubility of this pollutant into the aqueous phase where the bioprocess takes place. This research seeks to assess the performance of different non-aqueous phase liquids (NAPs): n-hexadecane (HEX), diethyl sebacate (DSE), 1,1,1,3,5,5,5-heptamethyl-trisiloxane (HTX), 2,2,4,4,6,8,8-heptamethylnonane (HNO), and high temperature silicone oil (SO) in chemical absorption-biological reduction (CABR) integrated systems. The results showed that HNO and HTX had the maximum gas-liquid mass transfer capacity, being 0.32 mol NO/kmol NAP and 0.29 mol NO/kmol NAP, respectively. When an aqueous phase was added to the system, the mass transfer gas-liquid of NO was increased, with HTX reaching a removal efficiency of 82 ± 3% NO with water, and 88 ± 6% with a phosphate buffer solution. All NAPs were tested for short-term toxicity assessment and resulted neither toxic nor inhibitory for the biological activity (denitrification). DSE was found to be biodegradable, which could limit its applicability in biological processes for gas treatment. Finally, in the CABR system tests, it was shown that NO elimination improved in a short time (30 min) when the three mass transfer vectors (HEX, HTX, HNO) were added to enriched denitrifying bacteria.

Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples

The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.

Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity

Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial communities. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation; however, the effect of antibiotic treatment on the diversity of indigenous microbial populations and the consequences on the performance of tissue culture is not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) shoots in vitro as well as the composition of the plant-associated microbiome. The study revealed that shoot cultivation on a medium supplemented with 250 mg L^-1 timentin resulted in 29 ± 4% reduced biomass accumulation and a 1.2-1.6-fold higher level of oxidative stress injury compared to the control samples. Moreover, the growth properties of shoots were only partially restored after transfer to a medium without the antibiotic. Microbiome analysis of the shoot samples using multivariable region-based 16S rRNA gene sequencing revealed a diverse microbial community in the control tobacco shoots, including 59 bacterial families; however, it was largely dominated by Mycobacteriaceae. Antibiotic treatment resulted in a decline in microbial diversity (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. These results imply that the diversity of the plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.