Early gut microbiome development may impact brain and behavioral development. Using a nonhuman primate model (Macaca mulatta), we investigated the association between social environments and the gut microbiome on infant neurodevelopment and cognitive function. Infant rhesus monkeys (n = 33) were either mother-peer-reared (MPR) or nursery-reared (NR). Neurodevelopmental outcomes, namely emotional responsivity, visual orientation, and motor maturity, were assessed with the Primate Neonatal Neurobehavioral Assessment (PNNA) at 14–30 days. Cognitive development was assessed through tasks evaluating infant reward association, cognitive flexibility, and impulsivity at 6–8 months. The fecal microbiome was quantified from rectal swabs via 16S rRNA sequencing. Factor analysis was used to identify “co-abundance factors” describing patterns of microbial composition. We used multiple linear regressions with AIC Model Selection and differential abundance analysis (MaAsLin2) to evaluate relationships between co-abundance factors, microbiome diversity, and neuro-/cognitive development outcomes. At 30 days of age, a gut microbiome co-abundance factor, or pattern, with high Prevotella and Lactobacillus (β = −0.88, p = 0.04, AIC Weight = 68%) and gut microbiome alpha diversity as measured by Shannon diversity (β = −1.33, p = 0.02, AIC Weight = 80%) were both negatively associated with infant emotional responsivity. At 30 days of age, being NR was also associated with lower emotional responsivity (Factor 1 model: β = −3.13, p < 0.01; Shannon diversity model: β = −3.77, p < 0.01). The infant gut microbiome, along with early-rearing environments, may shape domains of neuro-/cognitive development related to temperament.

Metabolic dietary patterns, including the Empirical Dietary Index for Hyperinsulinaemia (EDIH) and Empirical Dietary Inflammatory Pattern (EDIP), are known to impact multiple chronic diseases, but the role of the colonic microbiome in mediating such relationships is poorly understood. Among 1,610 adults with faecal 16S rRNA data in the TwinsUK cohort, we identified the microbiome profiles for EDIH and EDIP (from food frequency questionnaires) cross-sectionally using elastic net regression. We assessed the association of the dietary pattern-related microbiome profile scores with circulating biomarkers in multivariable-adjusted linear regression. In addition, we used PICRUSt2 to predict biological pathways associated with the enriched microbiome profiles, and further screened pathways for associations with the dietary scores in linear regression analyses. Microbiome profile scores developed with 32 (EDIH) and 15 (EDIP) genera were associated with higher insulin and homeostatic model assessment of insulin resistance. Six genera were associated with both dietary scores: Ruminococcaceae_UCG-008, Lachnospiraceae_UCG-008, Defluviitaleaceae_UCG-011 Anaeroplasma, inversely and Negativibacillus, Streptococcus, positively. Further, pathways in fatty acid biosynthesis, sugar acid degradation, and mevalonate metabolism were associated with insulinaemic and inflammatory diets. Dietary patterns that exert metabolic effects on insulin and inflammation may influence chronic disease risk by modulating gut microbial composition and function.

Host–bacterial communities (microbiomes) are influenced by a wide range of factors including host genotype and parasite exposure. However, few studies disentangle temporal and host-genotype-specific variation in microbiome response to infection across several host tissues. We experimentally exposed the freshwater crustacean Daphnia magna to its fungal parasite Metschnikowia bicuspidata and characterized changes in host–bacterial communities associated with the parasite's development within the host. We used 16S rRNA gene sequencing to assess bacterial communities of the host (a) 24 h (‘initial parasite exposure’) and (b) 10 days (‘successful infection’) after exposure to a standard dose of M. bicuspidata spores, in host guts, body tissue (excluding guts) and whole individuals. We also investigated whether bacterial community responses to parasite exposure varied by host genotype.

Parasite exposure did not immediately alter host gut bacterial communities, but drove host-genotype-specific changes in the bacterial community composition of whole individuals. We validated that these changes were not driven by shifts in bacterial communities of the culturing medium, due to the addition of the parasite spore solution. Successful infection (i.e. the proliferation of M. bicuspidata spores in the host body) reduced alpha diversity and shifted abundance of dominant bacterial orders in the gut. Moreover, it induced a host-genotype-specific changes in body bacterial community composition. Overall, bacterial community responses to parasite exposure and subsequent infection are complex: they occur in a host-genotype-dependent manner, differentially at distinct timepoints after parasite exposure, and in specific host tissue.

The relationship between nutrition and ageing is complex. The metabolism and synthesis of micronutrients within the gut microbiome can influence human health but is challenging to study. Furthermore, studying ageing in humans is time-consuming and difficult to control for environmental factors. Studies in model organisms can guide research efforts in this area. This review describes how the nematode Caenorhabditis elegans can be used to study how bacteria and diet influence ageing and inform follow-on studies in humans. It is known that certain bacteria accelerate ageing in C. elegans. This age-accelerating effect is prevented by inhibiting folate synthesis within the bacteria, and we propose that in the human microbiome, certain bacteria also accelerate ageing in a way that can be modulated by interfering with bacterial folate synthesis. Bacterial-derived folates do not promote ageing themselves; rather, ageing is accelerated by bacteria in some way, either through secondary metabolites or other bacterial activity, which is dependent on bacterial folate synthesis. In humans, it may be possible to inhibit bacterial folate synthesis in the human gut while maintaining healthy folate status in the body via food and supplementation. The supplement form of folic acid has a common breakdown product that can be used by bacteria to increase folate synthesis. Thus, supplementation with folic acid may not be good for health in certain circumstances such as in older people or those with an excess of proteobacteria in their microbiome. For these groups, alternative supplement strategies may be a safer way to ensure adequate folate levels.

Maternal diet may modulate human milk microbiota, but the effects of nutritional supplements are unknown. We examined the associations of prenatal diet and supplement use with milk microbiota composition. Mothers reported prenatal diet intake and supplement use using self-administered food frequency and standardised questionnaires, respectively. The milk microbiota was profiled using 16S rRNA gene sequencing. Associations of prenatal diet quality, dietary patterns, and supplement use with milk microbiota diversity and taxonomic structure were examined using Wilcoxon signed-rank tests and multivariable models adjusting for relevant confounders. A subset of 645 mothers participating in the CHILD Cohort Study (originally known as the Canadian Healthy Infant Longitudinal Development Study) provided one milk sample between 2 and 6 months postpartum and used prenatal multivitamin supplements ≥4 times a week. After adjusting for confounders, vitamin C supplement use was positively associated with milk bacterial Shannon diversity (β = 0.18, 95% CI = 0.05, 0.31) and Veillonella and Granulicatella relative abundance (β = 0.54; 95% CI = 0.05, 1.03 and β = 0.44; 95% CI = 0.04, 0.84, respectively), and negatively associated with Finegoldia relative abundance (β = –0.31; 95% CI = –0.63, –0.01). Fish oil supplement use was positively associated with Streptococcus relative abundance (β = 0.26; 95% CI = 0.03, 0.50). Prenatal diet quality and dietary patterns were not associated with milk microbiota composition. Prenatal vitamin C and fish oil supplement use were associated with differences in the milk microbiota composition. Future studies are needed to confirm our findings and elucidate mechanisms linking maternal supplement use to milk microbiota and child health.

Cocoa-derived flavanols (CDF) may act as prebiotics. However, evidence is inconsistent, and the duration and dose of CDF intake needed to elicit any prebiotic effect are undefined. This randomized, double-blind, crossover study determined the effects of short-term, high-dose dietary supplementation with CDF versus matched placebo on gut microbiota composition in 8 healthy adults. A single faecal sample was collected 8 d after supplementation with 900 mg/d CDF or placebo. Gut microbiota composition and Bifidobacterium spp. and Lactobacillus spp. abundance were measured as secondary outcomes by 16S ribosomal ribonucleic acid (rRNA) amplicon sequencing and quantitative polymerase chain reaction, respectively. No between-treatment differences in the relative or absolute abundance of Bifidobacterium spp. (Cohen’s d = 0.89, P = 0.22) or Lactobacillus spp. (Cohen’s d = 0.42, P = 0.65) were detected. Shannon diversity (Cohen’s d = 0.38, P = 0.04) and overall community richness (Cohen’s d = 0.34, P = 0.06) were lower following CDF supplementation versus placebo, but no between-treatment differences in β-diversity or taxa relative abundances were observed. Findings are not consistent with a clear prebiotic effect of this short-term, high-dose CDF supplementation strategy relative to placebo.

The effect of single dietary fibre (DF) on lowering uric acid (UA) level has been reported in the literature. However, the potential protective mechanism of DF against potassium oxybate-induced hyperuricaemia (HUA), as modelled by prophylactic administration, remains unclear. The data demonstrate that DF significantly decreased serum and cerebral tissue UA concentrations, inhibited xanthine oxidase expression and activity in the liver and reduced levels of creatinine and urea nitrogen in the serum. Additionally, it mitigated the deposition of amyloid-β in cerebral tissue. Correlation analysis showed that DF modulated the Toll-like receptor 4/NF-κB signalling pathway, attenuating oxidative stress and inflammatory responses in HUA mice. Additionally, DF helps to maintain the composition of the gut microbiota, reducing harmful Desulfovibrio and enriching beneficial Akkermansia and Ruminococcus populations. The results of the faecal metabolomics analysis indicate that DF facilitates the regulation of metabolic pathways involved in oxidative stress and inflammation. These pathways include pyrimidine metabolism, tryptophan metabolism, nucleotide metabolism and vitamin B6 metabolism. Additionally, the study found that DF has a preventive effect on anxiety-like behaviour induced by HUA. In summary, DF shows promise in mitigating HUA and cognitive deficits, primarily by modulating gut microbiota and metabolites.

Hospital placement is essential training for medical interns, involving shift work and high-pressure environments. This can increase physiological and psychological stress, which may be mediated by metabolites of microbial digestion(1). Nutrients of interest include those accessible to microbial digestion and associated with altered signalling within the microbiota-gut-brain axis (MGBA)(1). Fibre is fermented by gut microbes to produce short-chain fatty acids(2) and is associated with improved psychological outcomes(3). Tryptophan, a precursor to gut-derived serotonin(2), has been negatively associated with anxiety(4). Processed foods contain food additives, excess sugars, and saturated fats that may disrupt gut homeostasis(1) and impact psychological well-being(4). Lastly, total energy intake may determine the level of substrate available for microbial fermentation(2). Therefore, this research explores how microbiota-accessible food components interact with physical and psychological well-being in a cohort of medical interns undertaking their first-year of hospital placement. Participants were healthy medical interns, during first-year hospital placement (n = 21) from the Hunter New England Local Health District, NSW, Australia. Participants completed diet and wellbeing surveys at baseline and every 2 months over a 10-month period. 24-hour diet diaries were self-recorded from participants using a mobile application (Easy Diet Diary) and analysed using AusNut and the NOVA classification system of ultra-processed foods (ULP). Wellbeing surveys include depression, anxiety, stress scale (DASS), and PROMIS survey for mental (M), physical (P), and sleep well-being. Current data represents an ‘in-progress’ of the longitudinal data collection. This study utilised Spearman correlation and Tukey’s post hoc test for mixed methods analysis. From baseline to timepoint 3 (T3, 4 months) daily energy intake was consistent with cohort estimated energy requirements (EER). However, consumption ranged from 37% to 167% of EER, indicating a large variation of intakes. Energy consumed from ULP ranged from 30% to 34% (p = 0.6875). Baseline tryptophan intake (x¯ = 1139mg) was within the suggested target, whilst fibre intake (x¯ = 23g) was below the recommended intake. Neither saw significant changes from baseline to T3. Fibre intake was positively correlated with mental and physical well-being at baseline (x¯ = 23.1g, M: r = 0.474, p = 0.04, P: r = 0.608, p = 0.007), and timepoint 2 (x¯ = 31.5g, M: r = 0.647,p = 0.026, P: r = 0.780, p = 0.004) but not at T3. In addition, baseline consumption of sugar (x¯ = 18g) and poly-unsaturated fats (x¯ = 15g) were both negatively correlated with mental and physical well-being. Overall, no significant dietary changes were evident from baseline to mid-year collection in a first-year medical intern cohort during hospital placements. Fibre was significantly associated with mental and physical well-being, building on current understanding of fibre’s role in the MGBA. Planned metabolite analysis will explore the mechanisms of proposed microbiome-accessible nutrients alongside diet, well-being, and microbiota data. Findings from this study will identify how diet-microbiome interactions change under stress, with wider positive implications on intense workplace environments with the aim to preserve individual wellbeing.

Urban inhabitants spend upwards of 90% of their time indoors where building design and mechanical air-handling systems negatively impact air quality, microbiome diversity and health outcomes. Urban bioremediation infrastructure designed to improve indoor environmental quality by drawing air through photosynthesizing plants and metabolically diverse rhizospheres have been investigated since the 1960s; however, in-depth analysis of the potential impacts on indoor environments is required: (1) although recent evidence has illustrated human microbiome alteration and associated health benefits related to exposure to green wall systems, the mechanism(s) of diversification have not yet been established, (2) microbial metabolism and airborne chemical dynamics are extraordinarily complex and hypotheses pertaining to rhizosphere microorganisms metabolizing pollutants require more attention. To explore these areas, we applied a shotgun metagenomic approach to quantify microbial diversity and establish preliminary metabolic profiles within active green wall modules spanning a range of growth media and plant selections. Results indicate that fundamental design decisions, including hydroponic vs. organic growth media, support rhizosphere microbiomes with distinct diversity and metabolic profiles which could impact system performance. The described relationships indicate fundamental green infrastructure design represents an opportunity to “grow” indoor microbial diversity and metabolisms with potential benefits for human pollutant exposure and health outcomes.

Certified organic farming is a suite of regulated practices that can support social, economic, and ecological sustainability in agriculture. Despite the standardization and regulation of certifying bodies, practices adopted by organic farmers vary with potential heterogeneous effects on environmental outcomes. While it is accepted that beliefs can enable or constrain the adoption of farming practices, it remains unclear if variation in organic farmer beliefs mediates observed heterogeneity in practices and the ecology of farms. Communities of soil microorganisms that induce plant resistance and regulate insect herbivores offer a lens to explore the relationship between beliefs and practice adoption. Variation in insect herbivores across organic farms is common but none have studied the role of farmer beliefs in regulating pests through the soil microbiome. Herein, we hypothesized that variation in adoption of microbiome-supportive practices by organic farmers is driven by heterogeneity in their microbiome beliefs. We also investigate the importance of demographic variables and farm characteristics, compared to farmer beliefs, for adoption of practices that support the microbiome. To test our hypothesis, we surveyed the microbiome beliefs, farming practices, and motivations of 85 organic farmers in New York State, USA. We used affinity propagation to cluster farmers by their beliefs, and statistical models to evaluate variation in farming practice adoption and farmer motivations. Our survey received a 30.5% response rate, most organic farmers (≈96%) believed the soil microbiome was important for supporting plant defenses and reducing pests, and <16% believed their farming practices were unimportant for promoting beneficial microbiomes. Seven clusters of farmers were identified that varied in their microbiome beliefs. Among the clusters ≈42% of farmers believed on-farm management and external factors (e.g., climate change) were important for promoting the microbiome. These farmers used fewer pesticides and synthetic mulches, more pre-planting practices (e.g., solarization), and were more motivated to adopt new practices to support the microbiome than their peers. The most important factors motivating adoption were reductions in pests, increased yields, and biodiversity benefits. Beliefs, demographics, and farm characteristics (e.g., time in organic management) were correlated with similar suites of farming practices, but only beliefs predicted farmer motivations. Our study suggests beliefs are key to understanding farmer motivations and promoting organic farming system sustainability via the pest-suppressive microbiome. More broadly, we suggest the need for socio-ecological approaches that account for farmer beliefs when studying the adoption of conservation practices in agroecosystems.

Diversion of the faecal stream is associated with diversion colitis (DC). Preliminary studies indicate that microbiome dysbiosis contributes to its development and potentially treatment. This review aims to characterise these changes in the context of faecal diversion and identify their clinical impact. A systematic search was conducted using MEDLINE, EMBASE and CENTRAL databases using a predefined search strategy identifying studies investigating changes in microbiome following diversion. Findings reported according to PRISMA guidelines. Of 743 results, 6 met inclusion criteria. Five reported significantly decreased microbiome diversity in the diverted colon. At phylum level, decreases in Bacillota with a concomitant increase in Pseudomonadota were observed, consistent with dysbiosis. At genus level, studies reported decreases in beneficial lactic acid bacteria which produce short-chain fatty acid (SCFA), which inversely correlated with disease severity. Significant losses in commensals were also noted. These changes were seen to be partially reversible with restoration of bowel continuity. Changes within the microbiome were reflected by histopathological findings suggestive of intestinal dysfunction. Faecal diversion is associated with dysbiosis in the diverted colon which may have clinical implications. This is reflected in loss of microbiome diversity, increases in potentially pathogenic-associated phyla and reduction in SCFA-producing and commensal bacteria.

An associated microbiome of any host helps it in different metabolic processes ranging from the decomposition of food to the maturation of gametes. Organisms with a parasitic mode of life, though present at nutritious sites inside their host, maintain their own microbiome. Nevertheless, the comprehensive characterization and functionality of microbiome in parasitic organisms remain understudied. We selected two nematode parasites of Kashmir Merino sheep viz; Haemonchus contortus and Trichuris ovis based on their higher prevalence, difference in mode of nutrition, habitation site and effect on host. The objective of the study was to explore the bacteria associated with these parasitic nematodes of sheep. We adopted a 16S rRNA metagenomic sequencing approach to estimate and compare the bacterial communities present in these two nematode species. Nematode parasites from Kashmir Merino sheep were identified morphologically and confirmed with DNA characterization. H. contortus was dominated by phylum Proteobacteria (57%), Firmicutes (25%), Bacteroidota (15%) and Actinobacteriota (3%). Conversely, T. ovis showed Proteobacteria (78%) followed by Firmicutes (8%), Bacteroidota (8%), Actinobacteriota (1%), Fusobacteriota (1%) and other phyla (4%). This study provides a comprehensive account of the microbiome composition of H. contortus and T. ovis, both of which are highly prevalent among Kashmir Merino sheep. Additionally, T. ovis exhibited a greater bacterial diversity compared to H. contortus. Notably, these nematodes were found to harbor certain pathogenic bacteria. This study can further be carried forward in gaining insights into the complex relationship between the microbiota of a parasite and its pathogenicity, reproductive potential and host microbiome modification.

Research on the gut microbiome and mental health among children and adolescents is growing. This umbrella review provides a high-level overview of current evidence syntheses to amalgamate current research and inform future directions. Searches were conducted across seven databases for peer-reviewed pediatric (<18 years) review literature. Studies reporting gut microbiome composition and/or biotic supplementation on depression, bipolar disorder, anxiety, attention deficit hyperactivity disorder, autism spectrum disorder (ASD), or obsessive-compulsive disorder (OCD) were included. Deduplication and screening took place in Covidence. A sensitivity analysis was conducted to assess the degree of primary study overlap. Among the 39 included review studies, 23 (59%) were observational and 16 (41%) were interventional. Most reviews (92%) focused on ASD. Over half (56%) of the observational and interventional reviews scored low or critically low for methodological quality. A higher abundance of Clostridium clusters and a lower abundance of Bifidobacterium were consistently observed in ASD studies. Biotic supplementation was associated with ASD symptom improvement. Gut microbiome-mental health evidence syntheses in child and youth depression, anxiety, bipolar disorder, and OCD are lacking. Preliminary evidence suggests an association between specific microbiota and ASD symptoms, with some evidence supporting a role for probiotic supplementation ASD therapy.

The factors that influence parasite associated bacterial microbial diversity and the geographic distributions of bacteria are not fully understood. In an effort to gain a deeper understanding of the relationship between the bacterial diversity of Ctenocephalides fleas and host species and the external environment, we conducted a metagenetic analysis of 107 flea samples collected from 8 distinct sampling sites in South Africa. Pooled DNA samples mostly comprising of 2 or 3 individuals sampled from the same host, and belonging to the same genetic cluster, were sequenced using the Ion PGM™ Hi-Q™ Kit and the Ion 316™ Chip v2. Differences were detected in the microbiome compositions between Ctenocephalides felis, Ctenocephalides canis and Ctenocephalides connatus. Although based on a small sample, C. connatus occurring on wildlife harboured a higher bacterial richness when compared to C. felis on domestic animals. Intraspecific differences in the microbial OTU diversity were detected within C. f. felis that occurred on domestic cats and dogs. Different genetic lineages of C. f. felis were similar in microbial compositions but some differences exist in the presence or absence of rare bacteria. Rickettsia and Bartonella OTU's identified in South African cat fleas differ from those identified in the USA and Australia. Intraspecific microbial compositions also differ across geographic sampling sites. Generalized dissimilarity modelling showed that temperature and humidity are potentially important environmental factors explaining the pattern obtained.

The built environment contributes to global carbon dioxide emissions with carbon-emitting building materials and construction processes. While achieving carbon-neutral construction is not feasible with conventional construction methods, microbial-based construction processes were suggested over three decades ago to reduce carbon dioxide emissions. With time, questions regarding scaling, predictability, and the applicability of microbial growth and biomass production emerged and still needed to be resolved to allow manufacturing. Within this opinion, we will discuss what can be achieved not to ‘grow a building’ per se but to ‘grow environmentally friendly biocement’. Elaborate pathways leading to the formation of cementitious materials by genetically manipulatable microorganisms have been described so far, providing options to enhance the suitability of these pathways for construction with synthetic biology and bioconvergence. These processes can also be combined with additional beneficial properties of cement-producing organisms, such as antimicrobial properties and carbon fixation by photosynthesis. Therefore, while we cannot yet ‘grow a building’, we can grow and design biocement for the construction industry.

Risk of bias assessment is a critical step of any meta-analysis or systematic review. Given the low sample count of many microbiome studies, especially observational or cohort studies involving human subjects, many microbiome studies have low power. This increases the importance of performing meta-analysis and systematic review for microbiome research in order to enhance the relevance and applicability of microbiome results. This work proposes a method based on the ROBINS-I tool to systematically consider sources of bias in microbiome research seeking to perform meta-analysis or systematic review for microbiome studies.