It is well established that the gut microbiota plays an important role in host health and is perturbed by several factors including antibiotics. Antibiotic‐induced changes in microbial composition can have a negative impact on host health including reduced microbial diversity, changes in functional attributes of the microbiota, formation, and selection of antibiotic‐resistant strains making hosts more susceptible to infection with pathogens such as Clostridioides difficile. Antibiotic resistance is a global crisis and the increased use of antibiotics over time warrants investigation into its effects on microbiota and health. In this review, we discuss the adverse effects of antibiotics on the gut microbiota and thus host health, and suggest alternative approaches to antibiotic use.

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Dysbiosis of intestinal microflora has been postulated in ulcerative colitis (UC), which is characterized by imbalance of mucosal tissue associated bacterial communities. However, the specific changes in mucosal microflora during different stages of UC are still unknown. The aim of the current study was to investigate the changes in mucosal tissue associated microbiota during acute exacerbations and remission stages of UC. The mucosal microbiota associated with colon biopsy of 12 patients suffering from UC (exacerbated stage) and the follow-up samples from the same patients (remission stage) as well as non-IBD subjects was studied using 16S rRNA gene-based sequencing and quantitative PCR. The total bacterial count in patients suffering from exacerbated phase of UC was observed to be two fold lower compared to that of the non-IBD subjects (p = 0.0049, Wilcox on matched-pairs signed rank tests). Bacterial genera including Stenotrophomonas, Parabacteroides, Elizabethkingia, Pseudomonas, Micrococcus, Ochrobactrum and Achromobacter were significantly higher in abundance during exacerbated phase of UC as compared to remission phase. The alterations in bacterial diversity with an increase in the abnormal microbial communities signify the extent of dysbiosis in mucosal microbiota in patients suffering from UC. Our study helps in identifying the specific genera dominating the microbiota during the disease and thus lays a basis for further investigation of the possible role of these bacteria in pathogenesis of UC.

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Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life.

Purpose Brewers’ spent grain (BSG) represents the largest by-product of the brewing industry. Its utilisation as an animal feed has become less practical today; however, its high fibre and protein content make it a promising untapped resource for human nutrition. BSG contains mainly insoluble fibre. This fibre, along with protein, is trapped with the complex lignocellulosic cell structure and must be solubilised to release components which may be beneficial to health through modulation of the gut microbiota. Methods In this study, the application of a simultaneous saccharification and fermentation process for the extraction and solubilisation of arabinoxylan from BSG is demonstrated. Results Processing of the BSG was varied to modulate the physicochemical and molecular characteristic of the released arabinoxylan. The maximum level of arabinoxylan solubilisation achieved was approximately 21%, compared to the unprocessed BSG which contained no soluble arabinoxylan (AX). Concentration of the solubilised material produced a sample containing 99% soluble AX. Samples were investigated for their microbiome modulating capacity in in-vitro faecal fermentation trials. Many samples promoted increased Lactobacillus levels (approx. twofold). One sample that contained the highest level of soluble AX was shown to be bifidogenic, increasing the levels of this genus approx. 3.5-fold as well as acetate (p = 0.018) and propionate (p < 0.001) production. Conclusion The findings indicate that AX extracted from BSG has prebiotic potential. The demonstration that BSG is a source of functional fibre is a promising step towards the application of this brewing side-stream as a functional food ingredient for human nutrition.

Graphical abstract

The gut microbial community is known to influence the human health and disease state and is shaped by various factors since birth. It is now evident that understanding the alterations in these commensal microbes during crucial stages of life is of utmost importance to determine and predict the health status of an individual. To study the gut microbiota in two such vital stages, pregnancy and infancy, we analyzed gut microbial communities from 20 mother-infant dyads at different stages of pregnancy and early infancy. In total, we analyzed 80 fecal samples for profiling the gut microbial community using 16S rRNA gene-based sequencing. We observed no significant alterations in the gut bacterial diversity during pregnancy; however, significant alterations were observed during the period from birth to six months in infants, with a reduction in Staphylococcus and Enterococcus and an increase in Bifidobacterium and Streptococcus with a more stable microbial community at the age of six months.