Dietary Iron Intake Has Long-Term Effects on the Fecal Metabolome and Microbiome

Iron is essential for life, but its imbalances can lead to severe health implications. Iron deficiency is the most common nutrient disorder worldwide, and iron disregulation in early life has been found to cause long-lasting behavioral, cognitive, and neural effects. However, little is known about the effects of dietary iron on gut microbiome function and metabolism. In this study, we sought to investigate the impact of dietary iron on the fecal metabolome and microbiome by using mice fed with three diets with different iron content: an iron deficient, an iron sufficient (standard), and an iron overload diet for seven weeks. Additionally, we sought to understand whether any observed changes would persist past the 7-week period of diet intervention. To assess this, all feeding groups were switched to a standard diet, and this feeding continued for an additional 7 weeks. Analysis of the fecal metabolome revealed that iron overload and deficiency significantly alter levels of peptides, nucleic acids, and lipids, including di- and tri-peptides containing branched-chain amino acids, inosine and guanosine, and several microbial conjugated bile acids. The observed changes in the fecal metabolome persist long after the switch back to a standard diet, with the cecal gut microbiota composition and function of each group distinct after the 7-week standard diet wash-out. Our results highlight the enduring metabolic consequences of nutritional imbalances, mediated by both host and gut microbiome, which persist after returning to original standard diets

microbeMASST: A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

microbeMASST, a taxonomically informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbe-derived metabolites and relative producers without a priori knowledge will vastly enhance the understanding of microorganisms’ role in ecology and human health

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms’ role in ecology and human health

Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces

A bacterial strain designated L2-7(T), phylogenetically related to Eubacterium hallii DSM 3353(T), was previously isolated from infant faeces. The complete genome of strain L2-7(T) contains eight copies of the 16S rRNA gene with only 98.098.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii. The next closest validly described species is Anaerostipes hadrus DSM 3319(T) (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7(T) to be a novel species, related to type strain E. hallii DSM 3353(T). The experimentally observed DNA-DNA hybridization value between strain L2-7(T) and E. hallii DSM 3353(T) was 26.25 %, close to that calculated from the genomes (34.3 %). The G+C content of the chromosomal DNA of strain L2-7(T) was 38.6 mol%. The major fatty acids were C-16(:0), C-16(:1) cis9 and a component with summed feature 10 (C-10(:1) c11/t9/t6c). Strain L2-7(T) had higher amounts of C-16:0 (30.6 %) compared to E. hallii DSM 3353(T) (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E. hallii DSM 3353(T). Furthermore, 16S rRNA gene phylogenetic analysis advocates that E. hallii DSM 3353(T) is misclassified, and its reclassification as a member of the family Lachnospiraceae is necessary. Using a polyphasic approach, we propose that E. hallii (=DSM 3353(T)=ATCC 27751(T)) be reclassified as the type strain of a novel genus Anaerobutyricum sp. nov., comb. nov. and we propose that strain L2-7(T) should be classified as a novel species, Anaerobutyricum soehngenii sp. nov. The type strain is L2-7(T) (=DSM 17630(T) =KCIC 15707(T)).Peer reviewe

Casein intake post weaning modulates gut microbial, metabolic and behavioral profiles in rats

The postnatal period is critical for brain and behavioral development and it is sensitive to environmental stimuli, such as nutrition. Prevention of weaning from maternal milk was previously shown to result in stress-induced immobility during the forced swim test (FST), indicative of depressive-like behavior, accompanied by neurochemical, gut microbial and metabolic alterations in rats. Separately, weaning was also found to act as a developmental trigger for a population of opioid receptor subtypes, an effect dependent on loss of dietary casein. In the present study, we explore the impact of exposure to the casein component of milk, and its two major genetic variants A1 and A2 β-casein, beyond weaning age. Rats exposed to casein-rich and casein-free milk, as well as to commercialized milk, containing a mixture of A1 and A2 β-casein, or exclusively A2 β-casein milk, from postnatal day (PND) 21 to PND25 were assessed for immobility behavior during the FST. Casein-rich and A1 β-casein containing milk but not casein-free and A2 β-casein milk increased stress-induced immobility compared to weaned control animals. This was concomitant with an increased abundance of bacteria from the Clostridium histolyticum group in the caecum and colon of the casein-rich group, region specific alterations of µ-opioid and oxytocin receptors in the brain, as well as modifications in urinary biochemical profiles. The A1 β-casein group additionally displayed a strong association between altered gut microbial metabolites in urine and brain metabolites. Our findings suggest that exposure to milk casein, in particular to A1 β-casein, beyond weaning age enhances stress-induced immobility during the FST, promoting a depressive-like phenotype, via a possible gut-brain axis dependent mechanism

Early-life differences in the gut microbiota composition and functionality of infants at elevated likelihood of developing autism spectrum disorder

Evidence from cross-sectional human studies, and preliminary microbial-based intervention studies, have implicated the microbiota-gut-brain axis in the neurobiology of autism spectrum disorder (ASD). Using a prospective longitudinal study design, we investigated the developmental profile of the fecal microbiota and metabolome in infants with (n = 16) and without (n = 19) a family history of ASD across the first 36 months of life. In addition, the general developmental levels of infants were evaluated using the Mullen Scales of Early Learning (MSEL) test at 5 and 36 months of age, and with ADOS-2 at 36 months of age. At 5 months of age, infants at elevated-likelihood of ASD (EL) harbored less Bifidobacterium and more Clostridium and Klebsiella species compared to the low-likelihood infants (LL). Untargeted metabolic profiling highlighted that LL infants excreted a greater amount of fecal & gamma;-aminobutyric acid (GABA) at 5 months, which progressively declined with age. Similar age-dependent patterns were not observed in the EL group, with GABA being consistently low across all timepoints. Integrated microbiome-metabolome analysis showed a positive correlation between GABA and Bifidobacterium species and negative associations with Clostridium species. In vitro experiments supported these observations demonstrating that bifidobacteria can produce GABA while clostridia can consume it. At the behavioral level, there were no significant differences between the EL and LL groups at 5 months. However, at 36 months of age, the EL group had significantly lower MSEL and ADOS-2 scores compared to the LL group. Taken together, the present results reveal early life alterations in gut microbiota composition and functionality in infants at elevated-likelihood of ASD. These changes occur before any behavioral impairments can be detected, supporting a possible role for the gut microbiota in emerging behavioral variability later in life

Transfer of antibiotics and their metabolites in human milk: Implications for infant health and microbiota.

Antibiotics are an essential tool for perinatal care. While antibiotics can play a life-saving role for both parents and infants, they also cause collateral damage to the beneficial bacteria that make up the host gut microbiota. This is especially true for infants, whose developing gut microbiota is uniquely sensitive to antibiotic perturbation. Emerging evidence suggests that disruption of these bacterial populations during this crucial developmental window can have long-term effects on infant health and development. Although most current studies have focused on microbial disruptions caused by direct antibiotic administration to infants or prenatal exposure to antibiotics administered to the mother, little is known about whether antibiotics in human milk may pose similar risks to the infant. This review surveys current data on antibiotic transfer during lactation and highlights new methodologies to assess drug transfer in human milk. Finally, we provide recommendations for future work to ensure antibiotic use in lactating parents is safe and effective for both parents and infants

A Complete Pipeline for Untargeted Urinary Volatolomic Profiling with Sorptive Extraction and Dual Polar and Nonpolar Column Methodologies Coupled with Gas Chromatography Time-of-Flight Mass Spectrometry

Volatolomics offers an opportunity for noninvasive detection and monitoring of human disease. While gas chromatography-mass spectrometry (GC-MS) remains the technique of choice for analyzing volatile organic compounds (VOCs), barriers to wider adoption in clinical practice still exist, including: sample preparation and introduction techniques, VOC extraction, throughput, volatolome coverage, biological interpretation, and quality control (QC). Therefore, we developed a complete pipeline for untargeted urinary volatolomic profiling. We optimized a novel extraction technique using HiSorb sorptive extraction, which exhibited high analytical performance and throughput. We achieved a broader VOC coverage by using HiSorb coupled with a set of complementary chromatographic methods and time-of-flight mass spectrometry. Furthermore, we developed a data preprocessing strategy by evaluating internal standard normalization, batch correction, and we adopted strict QC measures including removal of nonlinearly responding, irreproducible, or contaminated metabolic features, ensuring the acquisition of high-quality data. The applicability of this pipeline was evaluated in a clinical cohort consisting of pancreatic ductal adenocarcinoma (PDAC) patients (n = 28) and controls (n = 33), identifying four urinary candidate biomarkers (2-pentanone, hexanal, 3-hexanone, and p-cymene), which can successfully discriminate the cancer and noncancer subjects. This study presents an optimized, high-throughput, and quality-controlled pipeline for untargeted urinary volatolomic profiling. Use of the pipeline to discriminate PDAC from control subjects provides proof of principal of its clinical utility and potential for application in future biomarker discovery studies

Obesity and ethnicity alter gene expression in skin

Obesity is accompanied by dysfunction of many organs, but effects on the skin have received little attention. We studied differences in epithelial thickness by histology and gene expression by Affymetrix gene arrays and PCR in the skin of 10 obese (BMI 35-50) and 10 normal weight (BMI 18.5-26.9) postmenopausal women paired by age and ethnicity. Epidermal thickness did not differ with obesity but the expression of genes encoding proteins associated with skin blood supply and wound healing were altered. In the obese, many gene expression pathways were broadly downregulated and subdermal fat showed pronounced inflammation. There were no changes in skin microbiota or metabolites. African American subjects differed from European Americans with a trend to increased epidermal thickening. In obese African Americans, compared to obese European Americans, we observed altered gene expression that may explain known differences in water content and stress response. African Americans showed markedly lower expression of the gene encoding the cystic fibrosis transmembrane regulator characteristic of the disease cystic fibrosis. The results from this preliminary study may explain the functional changes found in the skin of obese subjects and African Americans.</p

Author correction: obesity and ethnicity alter gene expression in skin

Daniel Butler was omitted from the author list in the original version of this Article. The Author contributions section now reads: “J.M.W. designed, conducted, and contributed to the writing of the manuscript, prepared Fig. 1. S.G. evaluated and did statistical analysis on the skin and fat samples, prepared Figs. 2–9. J.O.A. evaluated and contributed to writing the manuscript. D.B prepared and sequenced DNA libraries for the skin microbiota data, and wrote the applicable parts of the methods section. C.M. analyzed and wrote up the skin microbiota data, prepared Fig. 10. All authors have read the manuscript and approved its contents. D.D. analyzed and wrote up the skin microbiota data. S.Z. ran and analyzed the skin metabolite data. J.S. assisted in design, analysis and wrote up the skin metabolite data. J.K. assisted in analysis write up of skin and fat data. J.L.B. assisted in analysis, interpretation and writing of the manuscript. P.R.H. designed, analyzed, interpreted the data, and was the primary author of the manuscript.” This has been corrected in the PDF and HTML versions of the Article, and in the accompanying Supplementary Information file.</p