Addressing the gut microbiome and implications for obesity

Identification of the gut microbiota as an environmental factor that modulates obesity and metabolic diseases has provided the medical and functional food industry with new targets to treat metabolic diseases. However, only limited knowledge about the mechanisms by which the gut microbiota contributes to these lifestyle diseases are known. The gut microbiota is involved in energy harvest from the diet, modulation of endocrine signalling, and promoting metabolic inflammation. This review will discuss how the gut microbiota is altered in obesity, some of the mechanisms by which it promotes disease development, and how pre- and probiotics may be used to improve metabolic diseases.     

Separation of sunscreens in skincare creams using greener high-temperature liquid chromatography and subcritical water chromatography

In this study, high-temperature liquid chromatographic (HTLC) and subcritical water chromatographic (SBWC) separations of sunscreens contained in skincare creams were achieved at temperatures ranging from 90 to 250°C. The columns employed in this work include a ZirChrom-DiamondBond-C18, a XTerra MS C18 and a XBridge C18 column. The quantity of methanol consumed by the greener HTLC sunscreen methods developed in this project is significantly reduced although the HTLC separation at this stage is not as efficient as that achieved by traditional HPLC. SBWC separation of sunscreens was also achieved on the XTerra MS C18 and the XBridge C18 columns using pure water at 230-250°C. Methanol was eliminated in the SBWC methods developed in this study.     

Longitudinal changes of human milk oligosaccharides,breastmilk microbiome and infant gut microbiome are associated with maternal characteristics

Human milk oligosaccharides (HMOs) play an important role in infant health. This study aimed to investigate the association of maternal characteristics with HMOs, human breastmilk (HBM) microbiome and infant gut microbiome over the first three months of lactation. Chinese mothers and infant pairs (n = 110) were included in this prospective cohort. Secretor status linked with α1,2-fucosyltransferase expression was determined by the presence of total α1,2-fucosylated HMOs in HBM for 75.8% of the mothers. The concentration of dominant HMOs significantly decreased over three months except for 3’-fucosyllactose. In addition to the elevated levels of α1,2-fucosylated HMOs, other neutral HMOs significantly reduced in secretors milk. Alpha-diversity of HBM and infant gut microbiome significantly increased over time, and an elevated abundance of Bifidobacterium and decreased levels of Streptococcus, Staphylococcus and Clostridium in the infant gut microbiota were noted. Multi-association analysis indicated maternal age and body mass index significantly correlated with specific HMOs and infant growth. Our study provides pivotal data on Chinese HMOs distribution profile, and their association with maternal characteristics and the infant gut microbiome.     

Scientific characterization of subclinical skin changes by noninvasive biophysical methods for development of more efficacious skincare products

In 1966, after finishing only my first year of a residency program, I went to the US to study for 2.5 years with Dr Albert M. Kligman the analysis of functional properties of various skin changes in vivo using aged skin, various types of dermatitis and topically applied steroid-induced atrophy as experimental models. Ten years later, I luckily found that measurements of high frequency conductance and capacitance of the skin enable us to evaluate the skin surface hydration state that determines the softness and smoothness of the skin and in particular to detect even subtle skin changes induced by changes in our environmental or by the application of skincare products and cosmetics. Employing such noninvasive biophysical instruments, I have analyzed the functional properties of normal and abnormal skin changes including subclinical skin changes such as atopic xerosis, senile xerosis, scars and effects of various topical and systemic agents. From these studies it became apparent that as long as a certain level of barrier function was retained skin surface hydration is a more important factor for enjoying a good quality of life. We also succeeded in confirming the effect of corneotherapy, the term so pertinently suggested by Dr Kligman for the beneficial effects of skincare products. We could show that their daily application definitely improves the condition of subclinical skin problems. Further progress in such instrumental analysis of skin properties will greatly aid us in the future in selecting a more desirable skincare product on an individual basis.     

Understanding the effects of dietary components on the gut microbiome and human health

Food Science and Biotechnology - The gut microbiome is the complex microbial ecosystem found in the gastrointestinal tract of humans and animals. It plays a vital role in host development,...     

Effects of lactic acid-producing bacteria as direct-fed microbials on the ruminal microbiome

The objective of this study was to evaluate ruminal microbiome changes associated with feeding Lactobacillus plantarum GB-LP1 as direct-fed microbials (DFM) in high-producing dairy cow diets. A dual-flow continuous culture system was used in a replicated 4 × 4 Latin square design. A basal diet was formulated to meet the requirements of a cow producing 45 kg of milk per day (16% crude protein and 28% starch). There were 4 experimental treatments: the basal diet without any DFM (CTRL); a mixture of Lactobacillus acidophilus, 1 × 10⁹ cfu/g, and Propionibacterium freudenreichii, 2 × 10⁹ cfu/g [MLP = 0.01% of diet dry matter (DM)]; and 2 different levels of L. plantarum, 1.35 × 10⁹ cfu/g (L1 = 0.05% and L2 = 0.10% of diet DM). Bacterial samples were collected from the fluid and particulate effluents before feeding and at 2, 4, 6, and 8 h after feeding; a composite of all time points was made for each fermentor within their respective fractionations. Bacterial community composition was analyzed through sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequenced data were analyzed on DADA2, and statistical analyses were performed in R (RStudio 3.0.1, https://www.r-project.org/) and SAS 9.4 (SAS Institute Inc.); orthogonal contrasts were used to compare treatments. Different than in other fermentation scenarios (e.g., silage or beef cattle high-grain diets), treatments did not affect pH or lactic acid concentration. Effects were mainly from overall DFM inclusion, and they were mostly observed in the fluid phase. The relative abundance of the phylum Firmicutes, family Lachnospiraceae, and 6 genera decreased with DFM inclusion, with emphasis on Butyrivibrio_2, Saccharofermentans, and Ruminococcus_1 that are fibrolytic and may display peptidase activity during fermentation. Lachnospiraceae_AC2044_group and Lachnospiraceae_XPB1014_group also decreased in the fluid phase, and their relative abundances were positively correlated with NH₃-N daily outflow from the fermentors. Specific effects of MLP and L. plantarum were mostly in specific bacteria associated with proteolytic and fibrolytic functions in the rumen. These findings help to explain why, in the previous results from this study, DFM inclusion decreased NH₃-N concentration without altering pH and lactic acid concentration.     

Effect of pegbovigrastim administration on the microbiome found in the vagina of cows postpartum

The objective of this study was to evaluate the effect of pegbovigrastim (PEG) treatment of peripartum Holstein cows on the microbiome found in the vagina postpartum using sequencing of the 16S rRNA gene. A subset of cows was randomly sampled from a larger study where cows had been randomly assigned to 1 of 2 treatments: pegbovigrastim (PEG) or untreated control (CTR). The PEG-treated cows received a subcutaneous injection containing 15 mg of pegbovigrastim 7 d before expected calving and a second injection within 24 h of calving. Vaginal samples from 97 PEG-treated and 98 CTR cows were collected at calving, 7 ± 3, and 35 ± 3 d in milk (0, 7, and 35 DIM). Metritis was diagnosed at 7 ± 3 DIM and purulent vaginal discharge (PVD) at 35 ± 3 DIM. The PEG treatment did not alter the vaginal microbiome. Principal coordinate analysis (PCoA) showed that metritic cows had a dissimilar vaginal microbiome compared with cows that did not develop metritis, particularly at 7 but also at 35 DIM. This difference was characterized by higher relative abundance of Porphyromonas and Bacteroides and a lower relative abundance of Ureaplasma, Ruminococcaceae, and Clostridiales at 7 DIM, and a higher relative abundance of Ureaplasma and a lower relative abundance of Pasteurellaceae at 35 DIM. Based on PCoA, we observed that cows that developed PVD had a dissimilar vaginal microbiome compared with cows that did not develop PVD, particularly at 35 DIM but also at 7 DIM. This difference was characterized by a higher relative abundance of Bacteroides at 7 DIM and higher relative abundance of Fusobacterium and Bacteroides at 35 DIM. Cows that developed metritis and PVD also had higher relative abundance of Fusobacterium and Bacteroides at 0 DIM. Furthermore, the Chao1 and Shannon indices were decreased in metritic cows at 7 DIM and in PVD cows at 7 and 35 DIM. In summary, PEG treatment had no effect on the vaginal microbiome, and uterine disease was associated with major changes in the microbiome found in the vagina postpartum.     

Wine microbiome: A dynamic world of microbial interactions

Most fermented products are generated by a mixture of microbes. These microbial consortia perform various biological activities responsible for the nutritional, hygienic, and aromatic qualities of the product. Wine is no exception. Substantial yeast and bacterial biodiversity is observed on grapes, and in both must and wine. The diverse microorganisms present interact throughout the winemaking process. The interactions modulate the hygienic and sensorial properties of the wine. Many studies have been conducted to elucidate the nature of these interactions, with the aim of establishing better control of the two fermentations occurring during wine processing. However, wine is a very complex medium making such studies difficult. In this review, we present the current state of research on microbial interactions in wines. We consider the different kinds of interactions between different microorganisms together with the consequences of these interactions. We underline the major challenges to obtaining a better understanding of how microbes interact. Finally, strategies and methodologies that may help unravel microbe interactions in wine are suggested.     

高通量测序技术在食品微生物检测中的应用

微生物超标及食源性致病菌引发的生物污染是影响国家公共卫生的主要因素。新一代的高通量测序技术因其高覆盖度、高灵敏度、高准确性和低成本等特点,已经作为食品安全检测最重要技术逐渐替代常规DNA诊断和微生物分型方法。本文通过综述测序的发展历史和二代测序原理及流程,着重论述以高通量测序为基础的16S rRNA、全基因组、宏基因组以及宏转录组分析在现代食品安全实验室中的应用,展现了高通量测序技术在食品微生物检测、食源性致病菌监控及食品发酵工艺等方面的巨大优势。     

食用菌多糖调控肠道菌群研究进展

多糖是食用菌的主要活性物质之一,具有抗氧化、抗肿瘤、抗炎、免疫调节等生物活性。文章从食用菌多糖的功效与结构、人体肠道菌群组成、分布与功能以及食用菌多糖如何调控肠道菌群影响人体健康方面进行了综述,同时对食用菌多糖的后续研究提出了建议。     

Industrial application of green chromatography - II. Separation and analysis of preservatives in skincare products using subcritical water chromatography

Several high-temperature liquid chromatography (HTLC) and subcritical water chromatography (SBWC) methods have been successfully developed in this study for separation and analysis of preservatives contained in Olay skincare creams. Efficient separation and quantitative analysis of preservatives have been achieved on four commercially available ZirChrom and Waters XBridge columns at temperatures ranging from 100 to 200°C. The quantification results obtained by both HTLC and SBWC methods developed for preservatives analysis are accurate and reproducible. A large number of replicate HTLC and SBWC runs also indicate no significant system building-up or interference for skincare cream analysis. Compared with traditional HPLC separation carried out at ambient temperature, the HTLC methods can save up to 90% methanol required in the HPLC mobile phase. However, the SBWC methods developed in this project completely eliminated the use of toxic organic solvents required in the HPLC mobile phase, thus saving a significant amount of money and making the environment greener. Although both homemade and commercial systems can accomplish SBWC separations, the SBWC methods using the commercial system for preservative analysis are recommended for industrial applications because they can be directly applied in industrial plant settings.     

Bacterial community structure in the drinking water microbiome is governed by filtration processes

The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.     

Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing

Variation in the composition of microorganisms in the rumen (the rumen microbiome) of dairy cattle (Bos taurus) is of great interest because of possible links to methane emission levels. Feed additives are one method being investigated to reduce enteric methane production by dairy cattle. Here we report the effect of 2 methane-mitigating feed additives (grapemarc and a combination of lipids and tannin) on rumen microbiome profiles of Holstein dairy cattle. We used untargeted (shotgun) massively parallel sequencing of microbes present in rumen fluid to generate quantitative rumen microbiome profiles. We observed large effects of the feed additives on the rumen microbiome profiles using multiple approaches, including linear mixed modeling, hierarchical clustering, and metagenomic predictions. The effect on the fecal microbiome profiles was not detectable using hierarchical clustering, but was significant in the linear mixed model and when metagenomic predictions were used, suggesting a more subtle effect of the diets on the lower gastrointestinal microbiome. A differential representation analysis (analogous to differential expression in RNA sequencing) showed significant overlap in the contigs (which are genome fragments representing different microorganism species) that were differentially represented between experiments. These similarities suggest that, despite the different additives used, the 2 diets assessed in this investigation altered the microbiomes of the samples in similar ways. Contigs that were differentially represented in both experiments were tested for associations with methane production in an independent set of animals. These animals were not treated with a methane-mitigating diet, but did show substantial natural variation in methane emission levels. The contigs that were significantly differentially represented in response to both dietary additives showed a significant enrichment for associations with methane production. This suggests that these methane-mitigating diets have altered the rumen microbiome toward naturally low methane-emitting microbial profiles. The contig sequences are predominantly new and include Faecalibacterium spp. The contigs we have identified here are potential biomarkers for low-methane-emitting cattle.     

The bovine colostrum microbiome and its association with clinical mastitis

In an effort to characterize colostrum microbial diversity and its potential associations with early-lactation clinical mastitis, we used high-throughput sequencing of the 16S rRNA gene to investigate the bovine colostrum microbiome. A prospective observational study was conducted that included 70 Holstein cows; colostrum samples were collected from all 4 mammary gland quarters. Colostrum samples were categorized according to whether the quarter was diagnosed (CMC) or not diagnosed (NCMC) with clinical mastitis during the first 30 d postpartum. Colostrum samples were dominated by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria, and Tenericutes phyla, with the 6 most common taxa [order (o), family (f), and genus (g)] being g_Staphylococcus, g_Prevotella, f_Ruminococcaceae, o_Bacteroidales, o_Clostridiales, and g_Pseudomonas. The colostrum microbiota of primiparous cows was significantly richer (higher number of bacterial species) than that of multiparous cows, and differences in colostrum taxonomic structure between parities were also observed. The microbial community of NCMC samples of primiparous cows was significantly more diverse than that of CMC samples, and the relative abundances of the Tenericutes and Fusobacteria phyla as well as the Mycoplasma and Fusobacterium genera were significantly higher in NCMC than in CMC samples of primiparous cows. The colostrum core microbiome, defined as the bacterial taxa common to all colostrum samples examined, was composed of 20 taxa and included bacterial genera already known to be associated with mastitis (e.g., Staphylococcus, Mycoplasma, and Streptococcus spp.). Our results indicate that the colostrum microbiome of primiparous cows differs from that of multiparous cows, and it harbors some diversity and taxonomic markers of mammary gland health specific to primiparous cows only.     

The human microbiome and metabolomics: Current concepts and applications

The mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host–microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases. Also, identification of these metabolic fingerprints could give us clues as to how to manipulate the microbiome to promote health or treat diseases. This review provides an overview of our current knowledge of the microbiome and metablomics, applications and the future perspectives.