Publications by authors named "Danielle G Lemay"

46 Publications

Machine Learning Identifies Stool pH as Predictor of Bone Mineral Density in Healthy Multi-Ethnic U.S. Adults.

J Nutr 2021 Jul 27. Epub 2021 Jul 27.

USDA ARS Western Human Nutrition Research Center, Davis, CA 95616, USA.

Background: A variety of modifiable and non-modifiable factors such as ethnicity, age, and diet have been shown to influence bone health. Previous studies are usually limited to analyses focused on the association of a few a priori variables or on a specific subset of the population.

Objective: Dietary, physiological, and lifestyle data were used to identify directly modifiable and non-modifiable variables predictive of bone mineral content (BMC) and bone mineral density (BMD) in healthy U.S. men and women using machine learning models.

Methods: Ridge, lasso, elastic net, and random forest models were used to predict whole-body, femoral neck, and spine BMC and BMD in healthy U.S. men and women ages 18-66 y, BMI 18-44 kg/m2 (n = 313) using non-modifiable anthropometric, physiological, and demographic variables, directly modifiable lifestyle (physical activity, tobacco use) and dietary (via food frequency questionnaire) variables, and variables approximating directly-modifiable behavior (circulating 25-hydroxycholecalciferol and stool pH).

Results: Machine learning models using non-modifiable variables explained more variation in BMC and BMD (highest R2 = 0.75) compared to when using only directly modifiable variables (highest R2 = 0.11). Machine learning models had better performance compared to multivariate linear regression, which had lower predictive value (highest R2 = 0.06) when using directly modifiable variables only. BMI, body fat %, height, and menstruation history were predictors of BMC and BMD. For directly modifiable features, betaine, cholesterol, hydroxyproline, menaquinone-4, dihydrophylloquinone, eggs, cheese, cured meat, refined grains, fruit juice, and alcohol consumption were predictors of BMC and BMD. Low stool pH, a proxy for fermentable fiber intake, was also predictive of higher BMC and BMD.

Conclusion: Modifiable factors, such as diet, explained less variation in the data compared to non-modifiable factors, such as age, sex, and ethnicity in healthy U.S. men and women. Low stool pH predicted higher BMC and BMD.Clinical trial: registered on clinicaltrials.gov (Identifier: NCT02367287).
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http://dx.doi.org/10.1093/jn/nxab266DOI Listing
July 2021

Effect of Manual Data Cleaning on Nutrient Intakes Using the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24).

Curr Dev Nutr 2021 Mar 2;5(3):nzab005. Epub 2021 Feb 2.

USDA Agricultural Research Service Western Human Nutrition Research Center, Davis, CA, USA.

Background: Automated dietary assessment tools such as ASA24 are useful for collecting 24-hour recall data in large-scale studies. Modifications made during manual data cleaning may affect nutrient intakes.

Objectives: We evaluated the effects of modifications made during manual data cleaning on nutrient intakes of interest: energy, carbohydrate, total fat, protein, and fiber.

Methods: Differences in mean intake before and after data cleaning modifications for all recalls and average intakes per subject were analyzed by paired -tests. The Chi-squared test was used to determine whether unsupervised recalls had more open-ended text responses that required modification than supervised recalls. We characterized food types of text response modifications. Correlations between predictive energy requirements, measured total energy expenditure (TEE), and mean energy intake from raw and modified data were examined.

Results: After excluding 11 recalls with invalidating technical errors, 1499 valid recalls completed by 393 subjects were included in this analysis. We found significant differences before and after modifications for energy, carbohydrate, total fat, and protein intakes for all recalls ( 0.05). Limiting to modified recalls, there were significant differences for all nutrients of interest, including fiber ( < 0.02). There was not a significantly greater proportion of text responses requiring modification for home compared with supervised recalls ( = 0.271). Predicted energy requirements correlated highly with TEE. There was no significant difference in correlation of mean energy intake with TEE for modified compared with raw data. Mean intake for individual subjects was significantly different for energy, protein, and fat intakes following cleaning modifications ( < 0.001).

Conclusions: Manual modifications can change mean nutrient intakes for an entire cohort and individuals. However, modifications did not significantly affect the correlation of energy intake with predictive requirements and measured expenditure. Investigators can consider their research question and nutrients of interest when deciding to make cleaning modifications.
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http://dx.doi.org/10.1093/cdn/nzab005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7965072PMC
March 2021

Technician-Scored Stool Consistency Spans the Full Range of the Bristol Scale in a Healthy US Population and Differs by Diet and Chronic Stress Load.

J Nutr 2021 Jun;151(6):1443-1452

USDA Agricultural Research Service Western Human Nutrition Research Center, Davis, CA, USA.

Background: Prior studies of adults with constipation or diarrhea suggest that dietary intake, physical activity, and stress may affect stool consistency. However, the influence of these factors is unresolved and has not been investigated in healthy adults.

Objectives: We assessed the relations of technician-scored stool consistency in healthy adults with self-reported diet, objectively monitored physical activity, and quantifiable markers of stress.

Methods: Stool consistency was scored by an independent technician using the Bristol Stool Form Scale (BSFS) to analyze samples provided by healthy adults, aged 18-65 y, BMI 18-44 kg/m2, in the USDA Nutritional Phenotyping Study (n = 364). A subset of participants (n = 109) were also asked to rate their sample using the BSFS. Dietary intake was assessed with two to three 24-h recalls completed at home and energy expenditure from physical activity was monitored using an accelerometer in the 7-d period preceding the stool collection. Stress was measured using the Wheaton Chronic Stress Inventory and allostatic load (AL). Statistical and machine learning analyses were conducted to determine which dietary, physiological, lifestyle, and stress factors differed by stool form.

Results: Technician-scored BSFS scores were significantly further (P = 0.003) from the central score (mean ± SEM distance: 1.41 ± 0.089) than the self-reported score (1.06 ± 0.086). Hard stool was associated with higher (P = 0.005) intake of saturated fat (13.8 ± 0.40 g/1000 kcal) than was normal stool (12.5 ± 0.30 g/1000 kcal). AL scores were lower for normal stool (2.49 ± 0.15) than for hard (3.07 ± 0.18) (P = 0.009) or soft stool (2.89 ± 0.18) (P = 0.049). Machine learning analyses revealed that various dietary components, physiological characteristics, and stress hormones predicted stool consistency.

Conclusions: Technician-scored stool consistency differed by dietary intake and stress hormones, but not by physical activity, in healthy adults.This trial was registered at clincialtrials.gov as NCT02367287.
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http://dx.doi.org/10.1093/jn/nxab019DOI Listing
June 2021

Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent.

Front Genet 2020 29;11:558762. Epub 2020 Oct 29.

UC Davis Genome Center, Davis, CA, United States.

Among people of European descent, the ability to digest lactose into adulthood arose via strong positive selection of a highly advantageous allele encompassing the lactase gene. Lactose-tolerant and intolerant individuals may have different disease risks due to the shared genetics of their haplotype block. Therefore, the overall objective of the study was to assess the genetic association of the lactase persistence haplotype to disease risk. Using data from the 1000Genomes project, we estimated the size of the lactase persistence haplotype block to be 1.9 Mbp containing up to 9 protein-coding genes and a microRNA. Based on the function of the genes and microRNA, we studied health phenotypes likely to be impacted by the lactase persistence allele: prostate cancer status, cardiovascular disease status, and bone mineral density. We used summary statistics from large genome-wide metanalyses-32,965 bone mineral density, 140,306 prostate cancer and 184,305 coronary artery disease subjects-to evaluate whether the lactase persistence allele was associated with these disease phenotypes. Despite the fact that previous work demonstrated that the lactase persistence haplotype block harbors increased deleterious mutations, these results suggest little effect on the studied disease phenotypes.
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http://dx.doi.org/10.3389/fgene.2020.558762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7658388PMC
October 2020

Reservoirs of antimicrobial resistance genes in retail raw milk.

Microbiome 2020 06 26;8(1):99. Epub 2020 Jun 26.

Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.

Background: It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw milk can cause foodborne illness and be a source of bacteria containing transferrable antimicrobial resistance genes (ARGs). To obtain a comprehensive understanding of the microbiome and antibiotic resistome in both raw and processed milk, we systematically analyzed 2034 retail milk samples including unpasteurized milk and pasteurized milk via vat pasteurization, high-temperature-short-time pasteurization, and ultra-pasteurization from the United States using complementary culture-based, 16S rRNA gene, and metagenomic sequencing techniques.

Results: Raw milk samples had the highest prevalence of viable bacteria which were measured as all aerobic bacteria, coliform, and Escherichia coli counts, and their microbiota was distinct from other types of milk. 16S rRNA gene sequencing revealed that Pseudomonadaceae dominated raw milk with limited levels of lactic acid bacteria. Among all milk samples, the microbiota remained stable with constant bacterial populations when stored at 4 °C. In contrast, storage at room temperature dramatically enriched the bacterial populations present in raw milk samples and, in parallel, significantly increased the richness and abundance of ARGs. Metagenomic sequencing indicated raw milk possessed dramatically more ARGs than pasteurized milk, and a conjugation assay documented the active transfer of bla, one ceftazidime resistance gene present in raw milk-borne E. coli, across bacterial species. The room temperature-enriched resistome differed in raw milk from distinct geographic locations, a difference likely associated with regionally distinct milk microbiota.

Conclusion: Despite advertised "probiotic" effects, our results indicate that raw milk microbiota has minimal lactic acid bacteria. In addition, retail raw milk serves as a reservoir of ARGs, populations of which are readily amplified by spontaneous fermentation. There is an increased need to understand potential food safety risks from improper transportation and storage of raw milk with regard to ARGs. Video Abstract.
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http://dx.doi.org/10.1186/s40168-020-00861-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320593PMC
June 2020

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes.

BMC Bioinformatics 2020 Feb 24;21(1):74. Epub 2020 Feb 24.

USDA ARS Western Human Nutrition Research Center, Davis, CA, 95616, USA.

Background: Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database. The ability to detect genes in short read sequences is dependent on pre- and post-sequencing decisions. The objective of the current study was to determine how library size selection, read length and format, protein database, e-value threshold, and sequencing depth impact gene-centric analysis of human fecal microbiomes when using DIAMOND, an alignment tool that is up to 20,000 times faster than BLASTX.

Results: Using metagenomes simulated from a database of experimentally verified protein sequences, we find that read length, e-value threshold, and the choice of protein database dramatically impact detection of a known target, with best performance achieved with longer reads, stricter e-value thresholds, and a custom database. Using publicly available metagenomes, we evaluated library size selection, paired end read strategy, and sequencing depth. Longer read lengths were acheivable by merging paired ends when the sequencing library was size-selected to enable overlaps. When paired ends could not be merged, a congruent strategy in which both ends are independently mapped was acceptable. Sequencing depths of 5 million merged reads minimized the error of abundance estimates of specific target genes, including an antimicrobial resistance gene.

Conclusions: Shotgun metagenomes of DNA extracted from human fecal samples sequenced using the Illumina platform should be size-selected to enable merging of paired end reads and should be sequenced in the PE150 format with a minimum sequencing depth of 5 million merge-able reads to enable detection of specific target genes. Expecting the merged reads to be 180-250 bp in length, the appropriate e-value threshold for DIAMOND would then need to be more strict than the default. Accurate and interpretable results for specific hypotheses will be best obtained using small databases customized for the research question.
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http://dx.doi.org/10.1186/s12859-020-3416-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7041091PMC
February 2020

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults.

J Nutr Biochem 2020 05 17;79:108340. Epub 2020 Jan 17.

Genome Center, University of California-Davis, Davis, California, United States; Foods for Health Institute, University of California, Davis, California, United States; USDA ARS Western Human Nutrition Research Center, Davis, California, United States. Electronic address:

Human milk oligosaccharides play a vital role in the development of the gut microbiome in the human infant. Although oligosaccharides derived from bovine milk (BMO) differ in content and profile with those derived from human milk (HMO), several oligosaccharide structures are shared between the species. BMO are commercial alternatives to HMO, but their fate in the digestive tract of healthy adult consumers is unknown. Healthy human subjects consumed two BMO doses over 11-day periods each and provided fecal samples. Metatranscriptomics of fecal samples were conducted to determine microbial and host gene expression in response to the supplement. Fecal samples were also analyzed by mass spectrometry to determine levels of undigested BMO. No changes were observed in microbial gene expression across all participants. Repeated sampling enabled subject-specific analyses: four of six participants had minor, yet statistically significant, changes in microbial gene expression. No significant change was observed in the gene expression of host cells exfoliated in stool. Levels of BMO excreted in feces after supplementation were not significantly different from baseline and were not correlated with dosage or expressed microbial enzyme levels. Collectively, these data suggest that BMO are fully fermented in the human gastrointestinal tract upstream of the distal colon. Additionally, the unaltered host transcriptome provides further evidence for the safety of BMO as a dietary supplement or food ingredient. Further research is needed to investigate potential health benefits of this completely fermentable prebiotic that naturally occurs in cow's milk.
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http://dx.doi.org/10.1016/j.jnutbio.2020.108340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233280PMC
May 2020

Nutrient Estimation from 24-Hour Food Recalls Using Machine Learning and Database Mapping: A Case Study with Lactose.

Nutrients 2019 Dec 13;11(12). Epub 2019 Dec 13.

Western Human Nutrition Research Center, USDA ARS, Davis, CA 95616, USA.

The Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) is a free dietary recall system that outputs fewer nutrients than the Nutrition Data System for Research (NDSR). NDSR uses the Nutrition Coordinating Center (NCC) Food and Nutrient Database, both of which require a license. Manual lookup of ASA24 foods into NDSR is time-consuming but currently the only way to acquire NCC-exclusive nutrients. Using lactose as an example, we evaluated machine learning and database matching methods to estimate this NCC-exclusive nutrient from ASA24 reports. ASA24-reported foods were manually looked up into NDSR to obtain lactose estimates and split into training ( = 378) and test ( = 189) datasets. Nine machine learning models were developed to predict lactose from the nutrients common between ASA24 and the NCC database. Database matching algorithms were developed to match NCC foods to an ASA24 food using only nutrients ("Nutrient-Only") or the nutrient and food descriptions ("Nutrient + Text"). For both methods, the lactose values were compared to the manual curation. Among machine learning models, the XGB-Regressor model performed best on held-out test data ( = 0.33). For the database matching method, Nutrient + Text matching yielded the best lactose estimates ( = 0.76), a vast improvement over the status quo of no estimate. These results suggest that computational methods can successfully estimate an NCC-exclusive nutrient for foods reported in ASA24.
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http://dx.doi.org/10.3390/nu11123045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950225PMC
December 2019

The fecal resistome of dairy cattle is associated with diet during nursing.

Nat Commun 2019 09 27;10(1):4406. Epub 2019 Sep 27.

Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, One Shields Ave., Davis, CA, 95616, USA.

Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.
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http://dx.doi.org/10.1038/s41467-019-12111-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765000PMC
September 2019

Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal.

J Nutr Biochem 2019 10 21;72:108209. Epub 2019 Jun 21.

USDA-ARS Western Human Nutrition Research Center, 430 West Health Sciences Dr., Davis, CA 95616; Department of Nutrition, University of California-Davis, One Shields Avenue, Davis, CA, 95616. Electronic address:

White blood cells are among the first responders to dietary components and their metabolites absorbed from the gut. The objective of this study was to determine the whole blood transcriptome response to high-fat challenge meals. A total of 45 fasting and postprandial (3-h and 6-h) whole blood transcriptomes from 5 subjects in a crossover intervention trial of a high-fat meal supplemented with placebo, blueberry powder or docosahexaenoic acid (DHA) were analyzed using RNA sequencing. Select target genes were validated by quantitative reverse-transcription polymerase chain reaction in 180 samples from 20 subjects. The largest contributor to variance was the subject (13,856 genes differentially expressed), followed by the subject on a specific day (2276 genes), followed by the subject's postprandial response (651 genes). After determining the nonsignificance of individual dietary treatments (blueberry, DHA, placebo), treatments were used as replicates to examine postprandial responses to a high-fat meal. The universal postprandial response (95 genes) was associated with lipid utilization, fatty acid beta-oxidation and circadian rhythms. Subject-specific postprandial responses were enriched for genes involved in the innate immune response, particularly those of pattern recognition receptors and their downstream signaling components. Genes involved in innate immune responses are differentially expressed in a subject-specific and time-dependent manner in response to the high-fat meals. These genes can serve as biomarkers to assess individual responsiveness to a high-fat diet in inducing postprandial inflammation. Furthermore, the dynamic temporal change in gene expression in postprandial blood suggests that monitoring these genes at multiple time points is necessary to reveal responders to dietary intervention.
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http://dx.doi.org/10.1016/j.jnutbio.2019.06.007DOI Listing
October 2019

Association of Lactase Persistence Genotypes (rs4988235) and Ethnicity with Dairy Intake in a Healthy U.S. Population.

Nutrients 2019 Aug 10;11(8). Epub 2019 Aug 10.

USDA ARS Western Human Nutrition and Research Center, Davis, CA 95616, USA.

Lactase persistence (LP) is a trait in which lactose can be digested throughout adulthood, while lactase non-persistence (LNP) can cause lactose intolerance and influence dairy consumption. One single nucleotide polymorphism (SNP ID: rs4988235) is often used as a predictor for dairy intake, since it is responsible for LP in people in European descent, and can occur in other ethnic groups. The objective of this study was to determine whether rs4988235 genotypes and ethnicity influence reported dairy consumption in the United States (U.S.). A food frequency questionnaire (FFQ) and multiple Automated Self-Administered 24-h recalls (ASA24) were used to measure habitual and recent intake, respectively, of total dairy, cheese, cow's milk, plant-based alternative milk, and yogurt in a multi-ethnic U.S. cohort genotyped for rs4988235. Within Caucasian subjects, LP individuals reported consuming more recent total dairy and habitual total cow's milk intake. For subjects of all ethnicities, LP individuals consumed more cheese (FFQ 0.043, ASA24 0.012) and recent total dairy (ASA24 0.005). For both dietary assessments, Caucasians consumed more cheese than all non-Caucasians (FFQ 0.036, ASA24 0.002) independent of genotype, as well as more recent intake of yogurt (ASA24 0.042). LP subjects consumed more total cow's milk than LNP, but only when accounting for whether subjects were Caucasian or not (FFQ 0.015). Fluid milk and alternative plant-based milk consumption were not associated with genotypes or ethnicity. Our results show that both LP genotype and ethnicity influence the intake of some dairy products in a multi-ethnic U.S. cohort, but the ability of rs4988235 genotypes to predict intake may depend on ethnic background, the specific dairy product, and whether intake is reported on a habitual or recent basis. Therefore, ethnicity and the dietary assessment method should also be considered when determining the suitability of rs4988235 as a proxy for dairy intake.
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http://dx.doi.org/10.3390/nu11081860DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723957PMC
August 2019

Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.

Microbiome 2019 03 18;7(1):41. Epub 2019 Mar 18.

Genome Center, University of California, Davis, California, USA.

Background: Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease.

Results: Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes.

Conclusions: The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.
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http://dx.doi.org/10.1186/s40168-019-0664-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423747PMC
March 2019

Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.

PLoS One 2019 9;14(1):e0210064. Epub 2019 Jan 9.

MIND Institute, University of California Davis, Sacramento, California, United States of America.

Over half of all children with autism spectrum disorders (ASD) have gastrointestinal (GI) co-morbidities including chronic constipation, diarrhea, and irritable bowel syndrome. The severity of these symptoms has been correlated with the degree of GI microbial dysbiosis. The study objective was to assess tolerability of a probiotic (Bifidobacterium infantis) in combination with a bovine colostrum product (BCP) as a source of prebiotic oligosaccharides and to evaluate GI, microbiome and immune factors in children with ASD and GI co-morbidities. This pilot study is a randomized, double blind, controlled trial of combination treatment (BCP + B. infantis) vs. BCP alone in a cross-over study in children ages 2-11 with ASD and GI co-morbidities (n = 8). This 12-week study included 5 weeks of probiotic-prebiotic supplementation, followed by a two-week washout period, and 5 weeks of prebiotic only supplementation. The primary outcome of tolerability was assessed using validated questionnaires of GI function and atypical behaviors, along with side effects. Results suggest that the combination treatment is well-tolerated in this cohort. The most common side effect was mild gassiness. Some participants on both treatments saw a reduction in the frequency of certain GI symptoms, as well as reduced occurrence of particular aberrant behaviors. Improvement may be explained by a reduction in IL-13 and TNF-α production in some participants. Although limited conclusions can be drawn from this small pilot study, the results support the need for further research into the efficacy of these treatments.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210064PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326569PMC
September 2019

The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium.

PLoS One 2018 22;13(8):e0201637. Epub 2018 Aug 22.

Genome Center, University of California Davis, Davis, California, United States of America.

Collaboration among scientists has a major influence on scientific progress. Such collaboration often results from scientific meetings, where scientists gather to present and discuss their research and to meet potential collaborators. However, most scientific meetings have inherent biases, such as the availability of research funding or the selection bias of professional societies that make it difficult to study the effect of the meeting per se on scientific productivity. To evaluate the effects of scientific meetings on collaboration and progress independent of these biases, we conducted a study of the annual symposia held by the International Milk Genomics Consortium (IMGC) over a 12-year period. In our study, we conducted permutation testing to analyze the effectiveness of the IMGC in facilitating collaboration and productivity in a community of milk scientists who were meeting attendees relative to non-attendees. Using the number of co-authorships on published papers as a measure of collaboration, our analysis revealed that scientists who attended the symposium were associated with more collaboration than were scientists who did not attend. Furthermore, we evaluated the scientific progress of consortium attendees by analyzing publication rate and article impact. We found that IMGC attendees, in addition to being more collaborative, were also more productive and influential than were non-attendees who published in the same field. The results of our study suggest that the annual symposium encouraged interactions among disparate scientists and increased research productivity, exemplifying the positive effect of scientific meetings on both collaboration and progress.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201637PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104928PMC
January 2019

SAMSA2: a standalone metatranscriptome analysis pipeline.

BMC Bioinformatics 2018 05 21;19(1):175. Epub 2018 May 21.

Genome Center, University of California, Davis, California, USA.

Background: Complex microbial communities are an area of growing interest in biology. Metatranscriptomics allows researchers to quantify microbial gene expression in an environmental sample via high-throughput sequencing. Metatranscriptomic experiments are computationally intensive because the experiments generate a large volume of sequence data and each sequence must be compared with reference sequences from thousands of organisms.

Results: SAMSA2 is an upgrade to the original Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) pipeline that has been redesigned for standalone use on a supercomputing cluster. SAMSA2 is faster due to the use of the DIAMOND aligner, and more flexible and reproducible because it uses local databases. SAMSA2 is available with detailed documentation, and example input and output files along with examples of master scripts for full pipeline execution.

Conclusions: SAMSA2 is a rapid and efficient metatranscriptome pipeline for analyzing large RNA-seq datasets in a supercomputing cluster environment. SAMSA2 provides simplified output that can be examined directly or used for further analyses, and its reference databases may be upgraded, altered or customized to fit the needs of any experiment.
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http://dx.doi.org/10.1186/s12859-018-2189-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963165PMC
May 2018

The Transcriptome of Estrogen-Independent Mammary Growth in Female Mice Reveals That Not All Mammary Glands Are Created Equally.

Endocrinology 2017 10;158(10):3126-3139

Department of Animal Science, University of California Davis, Davis, California 95616-8521.

Allometric growth of ducts in the mammary glands (MGs) is widely held to be estrogen dependent. We previously discovered that the dietary fatty acid trans-10, cis-12 conjugated linoleic acid (CLA) stimulates estrogen-independent allometric growth and terminal end bud formation in ovariectomized mice. Given the similar phenotype induced by estrogen and CLA, we investigated the shared and/or divergent mechanisms underlying these changes. We confirmed MG growth induced by CLA is temporally distinct from that elicited by estrogen. We then used RNA sequencing to compare the transcriptome of the MG during similar proliferative and morphological states. Both estrogen and CLA affected the genes involved in proliferation. The transcriptome for estrogen-treated mice included canonical estrogen-induced genes, including Pgr, Areg, and Foxa1. In contrast, their expression was unchanged by CLA. However, CLA, but not estrogen, altered expression of a unique set of inflammation-associated genes, consistent with stromal changes. This CLA-altered signature included increased expression of epidermal growth factor receptor (EGFR) pathway components, consistent with the demonstration that CLA-induced MG growth is EGFR dependent. Our findings highlight a unique role for diet-induced inflammation that underlies estrogen-independent MG development.
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http://dx.doi.org/10.1210/en.2017-00395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5659702PMC
October 2017

Tolerability and safety of the intake of bovine milk oligosaccharides extracted from cheese whey in healthy human adults.

J Nutr Sci 2017 20;6:e6. Epub 2017 Feb 20.

Department of Food Science and Technology, University of California Davis, Davis, CA 95616, USA.

Mechanistic research suggests a unique evolutionary relationship between complex milk oligosaccharides and cognate bifidobacteria enriched in breast-fed infants. Bovine milk oligosaccharides (BMO) were recently identified as structurally and functionally similar to human milk oligosaccharides. The present single-blind three-way crossover study is the first to determine the safety and tolerability of BMO consumption by healthy human participants ( 12) and its effects on faecal microbiota and microbial metabolism. Participants consumed each supplement (placebo-control; low- and high-BMO doses) for eleven consecutive days, followed by a 2-week washout period prior to initiating the next supplement arm. Low and high BMO doses were consumed as 25 and 35 % of each individual's daily fibre intake, respectively. Safety and tolerability were measured using standardised questionnaires on gut and stomach discomfort and stool consistency. Faecal extracts were profiled for bacterial populations by next-generation sequencing (NGS) and bifidobacteria presence was confirmed using quantitative PCR. Urine was analysed for changes in microbial metabolism using nuclear magnetic resonance spectroscopy (H-NMR). Consumption of both the low and high BMO doses was well tolerated and did not change stool consistency from baseline. Multivariate analysis of the NGS results demonstrated no change in faecal microbiota phyla among the placebo-control and BMO supplement groups. In conclusion, BMO supplementation was well tolerated in healthy adults and has the potential to shift faecal microbiota toward beneficial strains as part of a synbiotic treatment with probiotic cultures that selectively metabolise oligosaccharides.
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http://dx.doi.org/10.1017/jns.2017.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465862PMC
February 2017

The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia.

Sci Rep 2017 02 2;7:40932. Epub 2017 Feb 2.

Department of Food Science and Technology, University of California, Davis, CA, USA.

Multiple factors help shape the infant intestinal microbiota early in life. Environmental conditions such as the presence of bioactive molecules from breast milk dictate gut microbial growth and survival. Infants also receive distinct, personalized, bacterial exposures leading to differential colonization. Microbial exposures and gut environmental conditions differ between infants in different locations, as does the typical microbial community structure in an infant's gut. Here we evaluate potential influences on the infant gut microbiota through a longitudinal study on cohorts of breast-fed infants from the neighboring countries of Armenia and Georgia, an area of the world for which the infant microbiome has not been previously investigated. Marker gene sequencing of 16S ribosomal genes revealed that the gut microbial communities of infants from these countries were dominated by bifidobacteria, were different from each other, and were marginally influenced by their mother's secretor status. Species-level differences in the bifidobacterial communities of each country and birth method were also observed. These community differences suggest that environmental variation between individuals in different locations may influence the gut microbiota of infants.
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http://dx.doi.org/10.1038/srep40932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288704PMC
February 2017

A novel gene cluster allows preferential utilization of fucosylated milk oligosaccharides in Bifidobacterium longum subsp. longum SC596.

Sci Rep 2016 10 19;6:35045. Epub 2016 Oct 19.

Department of Viticulture &Enology, University of California, One Shields Ave. Davis, CA 95616, United States.

The infant intestinal microbiota is often colonized by two subspecies of Bifidobacterium longum: subsp. infantis (B. infantis) and subsp. longum (B. longum). Competitive growth of B. infantis in the neonate intestine has been linked to the utilization of human milk oligosaccharides (HMO). However, little is known how B. longum consumes HMO. In this study, infant-borne B. longum strains exhibited varying HMO growth phenotypes. While all strains efficiently utilized lacto-N-tetraose, certain strains additionally metabolized fucosylated HMO. B. longum SC596 grew vigorously on HMO, and glycoprofiling revealed a preference for consumption of fucosylated HMO. Transcriptomes of SC596 during early-stage growth on HMO were more similar to growth on fucosyllactose, transiting later to a pattern similar to growth on neutral HMO. B. longum SC596 contains a novel gene cluster devoted to the utilization of fucosylated HMO, including genes for import of fucosylated molecules, fucose metabolism and two α-fucosidases. This cluster showed a modular induction during early growth on HMO and fucosyllactose. This work clarifies the genomic and physiological variation of infant-borne B. longum to HMO consumption, which resembles B. infantis. The capability to preferentially consume fucosylated HMO suggests a competitive advantage for these unique B. longum strains in the breast-fed infant gut.
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http://dx.doi.org/10.1038/srep35045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069460PMC
October 2016

SAMSA: a comprehensive metatranscriptome analysis pipeline.

BMC Bioinformatics 2016 Sep 29;17(1):399. Epub 2016 Sep 29.

Genome Center, University of California - Davis, Davis, CA, USA.

Background: Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated computing cluster, or metagenome-based approaches that have not been fully evaluated for processing metatranscriptomic datasets. We created a new bioinformatics pipeline, designed specifically for metatranscriptome dataset analysis, which runs in conjunction with Metagenome-RAST (MG-RAST) servers. Designed for use by researchers with relatively little bioinformatics experience, SAMSA offers a breakdown of metatranscriptome transcription activity levels by organism or transcript function, and is fully open source. We used this new tool to evaluate best practices for sequencing stool metatranscriptomes.

Results: Working with the MG-RAST annotation server, we constructed the Simple Annotation of Metatranscriptomes by Sequence Analysis (SAMSA) software package, a complete pipeline for the analysis of gut microbiome data. SAMSA can summarize and evaluate raw annotation results, identifying abundant species and significant functional differences between metatranscriptomes. Using pilot data and simulated subsets, we determined experimental requirements for fecal gut metatranscriptomes. Sequences need to be either long reads (longer than 100 bp) or joined paired-end reads. Each sample needs 40-50 million raw sequences, which can be expected to yield the 5-10 million annotated reads necessary for accurate abundance measures. We also demonstrated that ribosomal RNA depletion does not equally deplete ribosomes from all species within a sample, and remaining rRNA sequences should be discarded. Using publicly available metatranscriptome data in which rRNA was not depleted, we were able to demonstrate that overall organism transcriptional activity can be measured using mRNA counts. We were also able to detect significant differences between control and experimental groups in both organism transcriptional activity and specific cellular functions.

Conclusions: By making this new pipeline publicly available, we have created a powerful new tool for metatranscriptomics research, offering a new method for greater insight into the activity of diverse microbial communities. We further recommend that stool metatranscriptomes be ribodepleted and sequenced in a 100 bp paired end format with a minimum of 40 million reads per sample.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041328PMC
http://dx.doi.org/10.1186/s12859-016-1270-8DOI Listing
September 2016

Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria.

Sci Rep 2015 Sep 4;5:13517. Epub 2015 Sep 4.

Department of Viticulture &Enology, One Shields Ave. Davis, CA 95616, United States.

Breast milk enhances the predominance of Bifidobacterium species in the infant gut, probably due to its large concentration of human milk oligosaccharides (HMO). Here we screened infant-gut isolates of Bifidobacterium longum subsp. infantis and Bifidobacterium bifidum using individual HMO, and compared the global transcriptomes of representative isolates on major HMO by RNA-seq. While B. infantis displayed homogeneous HMO-utilization patterns, B. bifidum were more diverse and some strains did not use fucosyllactose (FL) or sialyllactose (SL). Transcriptomes of B. bifidum SC555 and B. infantis ATCC 15697 showed that utilization of pooled HMO is similar to neutral HMO, while transcriptomes for growth on FL were more similar to lactose than HMO in B. bifidum. Genes linked to HMO-utilization were upregulated by neutral HMO and SL, but not by FL in both species. In contrast, FL induced the expression of alternative gene clusters in B. infantis. Results also suggest that B. bifidum SC555 does not utilize fucose or sialic acid from HMO. Surprisingly, expression of orthologous genes differed between both bifidobacteria even when grown on identical substrates. This study highlights two major strategies found in Bifidobacterium species to process HMO, and presents detailed information on the close relationship between HMO and infant-gut bifidobacteria.
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http://dx.doi.org/10.1038/srep13517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559671PMC
September 2015

Human milk oligosaccharides in premature infants: absorption, excretion, and influence on the intestinal microbiota.

Pediatr Res 2015 Dec 31;78(6):670-7. Epub 2015 Aug 31.

Department of Chemistry, University of California Davis, Davis, California.

Background: Human milk oligosaccharides (HMOs) shape the intestinal microbiota in term infants. In premature infants, alterations in the intestinal microbiota (dysbiosis) are associated with risk of necrotizing enterocolitis (NEC) and sepsis, and the influence of HMOs on the microbiota is unclear.

Methods: Milk, urine, and stool specimens from 14 mother-premature infant dyads were investigated by mass spectrometry for HMO composition. The stools were analyzed by next-generation sequencing to complement a previous analysis.

Results: Percentages of fucosylated and sialylated HMOs were highly variable between individuals but similar in urine, feces, and milk within dyads. Differences in urine and fecal HMO composition suggest variability in absorption. Secretor status of the mother correlated with the urine and fecal content of specific HMO structures. Trends toward higher levels of Proteobacteria and lower levels of Firmicutes were noted in premature infants of nonsecretor mothers. Specific HMO structures in the milk, urine, and feces were associated with alterations in fecal Proteobacteria and Firmicutes.

Conclusion: HMOs may influence the intestinal microbiota in premature infants. Specific HMOs, for example those associated with secretor mothers, may have a protective effect by decreasing pathogens associated with sepsis and NEC, while other HMOs may increase dysbiosis in this population.
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http://dx.doi.org/10.1038/pr.2015.162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689671PMC
December 2015

Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells.

BMC Microbiol 2015 Aug 25;15:172. Epub 2015 Aug 25.

Foods for Health Institute University of California, Davis, Davis, CA, 95616, USA.

Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). Two predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both of which include avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increases adhesion to intestinal cells and increases the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source-glucose, lactose, or HMO-on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis.

Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both downregulated genes in Caco-2 cells associated with chemokine activity.

Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.
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http://dx.doi.org/10.1186/s12866-015-0508-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4548914PMC
August 2015

Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants.

Microbiome 2015 10;3:13. Epub 2015 Apr 10.

Department of Food Science and Technology, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA ; Department of Viticulture and Enology, UC Davis, 1 Shields Avenue, Davis, CA 95616 USA ; Foods For Health Institute, UC Davis, 1 Peter J Shields Avenue, Davis, CA 95616 USA.

Background: Individuals with inactive alleles of the fucosyltransferase 2 gene (FUT2; termed the 'secretor' gene) are common in many populations. Some members of the genus Bifidobacterium, common infant gut commensals, are known to consume 2'-fucosylated glycans found in the breast milk of secretor mothers. We investigated the effects of maternal secretor status on the developing infant microbiota with a special emphasis on bifidobacterial species abundance.

Results: On average, bifidobacteria were established earlier and more often in infants fed by secretor mothers than in infants fed by non-secretor mothers. In secretor-fed infants, the relative abundance of the Bifidobacterium longum group was most strongly correlated with high percentages of the order Bifidobacteriales. Conversely, in non-secretor-fed infants, Bifidobacterium breve was positively correlated with Bifidobacteriales, while the B. longum group was negatively correlated. A higher percentage of bifidobacteria isolated from secretor-fed infants consumed 2'-fucosyllactose. Infant feces with high levels of bifidobacteria had lower milk oligosaccharide levels in the feces and higher amounts of lactate. Furthermore, feces containing different bifidobacterial species possessed differing amounts of oligosaccharides, suggesting differential consumption in situ.

Conclusions: Infants fed by non-secretor mothers are delayed in the establishment of a bifidobacteria-laden microbiota. This delay may be due to difficulties in the infant acquiring a species of bifidobacteria able to consume the specific milk oligosaccharides delivered by the mother. This work provides mechanistic insight into how milk glycans enrich specific beneficial bacterial populations in infants and reveals clues for enhancing enrichment of bifidobacterial populations in at risk populations - such as premature infants.
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http://dx.doi.org/10.1186/s40168-015-0071-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412032PMC
April 2015

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.

J Proteome Res 2015 May 6;14(5):2143-57. Epub 2015 Apr 6.

⊥Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, Massachusetts 02138, United States.

Milk has been well established as the optimal nutrition source for infants, yet there is still much to be understood about its molecular composition. Therefore, our objective was to develop and compare comprehensive milk proteomes for human and rhesus macaques to highlight differences in neonatal nutrition. We developed a milk proteomics technique that overcomes previous technical barriers including pervasive post-translational modifications and limited sample volume. We identified 1606 and 518 proteins in human and macaque milk, respectively. During analysis of detected protein orthologs, we identified 88 differentially abundant proteins. Of these, 93% exhibited increased abundance in human milk relative to macaque and include lactoferrin, polymeric immunoglobulin receptor, alpha-1 antichymotrypsin, vitamin D-binding protein, and haptocorrin. Furthermore, proteins more abundant in human milk compared with macaque are associated with development of the gastrointestinal tract, the immune system, and the brain. Overall, our novel proteomics method reveals the first comprehensive macaque milk proteome and 524 newly identified human milk proteins. The differentially abundant proteins observed are consistent with the perspective that human infants, compared with nonhuman primates, are born at a slightly earlier stage of somatic development and require additional support through higher quantities of specific proteins to nurture human infant maturation.
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http://dx.doi.org/10.1021/pr501243mDOI Listing
May 2015

Changes in intestinal barrier function and gut microbiota in high-fat diet-fed rats are dynamic and region dependent.

Am J Physiol Gastrointest Liver Physiol 2015 May 6;308(10):G840-51. Epub 2015 Mar 6.

Department of Anatomy, Physiology and Cell Biology, University of California Davis School of Veterinary Medicine, Davis, California;

A causal relationship between the pathophysiological changes in the gut epithelium and altered gut microbiota with the onset of obesity have been suggested but not defined. The aim of this study was to determine the temporal relationship between impaired intestinal barrier function and microbial dysbiosis in the small and large intestine in rodent high-fat (HF) diet-induced obesity. Rats were fed HF diet (45% fat) or normal chow (C, 10% fat) for 1, 3, or 6 wk; food intake, body weight, and adiposity were measured. Barrier function ex vivo using FITC-labeled dextran (4,000 Da, FD-4) and horseradish peroxidase (HRP) probes in Ussing chambers, gene expression, and gut microbial communities was assessed. After 1 wk, there was an immediate but reversible increase in paracellular permeability, decrease in IL-10 expression, and decrease in abundance of genera within the class Clostridia in the ileum. In the large intestine, HRP flux and abundance of genera within the order Bacteroidales increased with time on the HF diet and correlated with the onset of increased body weight and adiposity. The data show immediate insults in the ileum in response to ingestion of a HF diet, which were rapidly restored and preceded increased passage of large molecules across the large intestinal epithelium. This study provides an understanding of microbiota dysbiosis and gut pathophysiology in diet-induced obesity and has identified IL-10 and Oscillospira in the ileum and transcellular flux in the large intestine as potential early impairments in the gut that might lead to obesity and metabolic disorders.
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http://dx.doi.org/10.1152/ajpgi.00029.2015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437018PMC
May 2015

Comparative genomics reveals tissue-specific regulation of prolactin receptor gene expression.

J Mol Endocrinol 2015 Feb 30;54(1):1-15. Epub 2014 Oct 30.

Department of Animal ScienceGenome CenterUniversity of California Davis, 2335 Meyer Hall, One Shields Avenue, Davis, California 95616, USABaylor College of MedicineUSDA/ARS Children's Nutrition Research Center, 1100 Bates Street, Room 9022, Houston, Texas, USAUSDAARS, U.S. Meat Animal Research Center, PO Box 166, Clay Center, Nebraska 68933, USA.

Prolactin (PRL), acting via the PRL receptor (PRLR), controls hundreds of biological processes across a range of species. Endocrine PRL elicits well-documented effects on target tissues such as the mammary glands and reproductive organs in addition to coordinating whole-body homeostasis during states such as lactation or adaptive responses to the environment. While changes in PRLR expression likely facilitates these tissue-specific responses to circulating PRL, the mechanisms regulating this regulation in non-rodent species has received limited attention. We performed a wide-scale analysis of PRLR 5' transcriptional regulation in pig tissues. Apart from the abundantly expressed and widely conserved exon 1, we identified alternative splicing of transcripts from an additional nine first exons of the porcine PRLR (pPRLR) gene. Notably, exon 1.5 transcripts were expressed most abundantly in the heart, while expression of exon 1.3-containing transcripts was greatest in the kidneys and small intestine. Expression of exon 1.3 mRNAs within the kidneys was most abundant in the renal cortex, and increased during gestation. A comparative analysis revealed a human homologue to exon 1.3, hE1N2, which was also principally transcribed in the kidneys and small intestines, and an exon hE1N3 was only expressed in the kidneys of humans. Promoter alignment revealed conserved motifs within the proximal promoter upstream of exon 1.3, including putative binding sites for hepatocyte nuclear factor-1 and Sp1. Together, these results highlight the diverse, conserved and tissue-specific regulation of PRLR expression in the targets for PRL, which may function to coordinate complex physiological states such as lactation and osmoregulation.
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http://dx.doi.org/10.1530/JME-14-0212DOI Listing
February 2015

The human colostrum whey proteome is altered in gestational diabetes mellitus.

J Proteome Res 2015 Jan 1;14(1):512-20. Epub 2014 Dec 1.

National Institute of Health West Coast Metabolomics Center, ‡Genome Center, §Genome Center Proteomics Core Facility, ⊥Department of Food Science and Technology, and ¶Foods for Health Institute, University of California Davis , Davis, California 95616, United States.

Proteomics of human milk has been used to identify the comprehensive cargo of proteins involved in immune and cellular function. Very little is known about the effects of gestational diabetes mellitus (GDM) on lactation and breast milk components. The objective of the current study was to examine the effect of GDM on the expression of proteins in the whey fraction of human colostrum. Colostrum was collected from women who were diagnosed with (n = 6) or without (n = 12) GDM at weeks 24-28 in pregnancy. Colostral whey was analyzed for protein abundances using high-resolution, high-mass accuracy liquid chromatography tandem mass spectrometry. A total of 601 proteins were identified, of which 260 were quantified using label free spectral counting. Orthogonal partial least-squares discriminant analysis identified 27 proteins that best predict GDM. The power law global error model corrected for multiple testing was used to confirm that 10 of the 27 proteins were also statistically significantly different between women with versus without GDM. The identified changes in protein expression suggest that diabetes mellitus during pregnancy has consequences on human colostral proteins involved in immunity and nutrition.
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http://dx.doi.org/10.1021/pr500818dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286167PMC
January 2015

Sequencing the transcriptome of milk production: milk trumps mammary tissue.

BMC Genomics 2013 Dec 12;14:872. Epub 2013 Dec 12.

Genome Center, University of California Davis, 451 Health Sciences Dr, Davis, CA 95616, USA.

Background: Studies of normal human mammary gland development and function have mostly relied on cell culture, limited surgical specimens, and rodent models. Although RNA extracted from human milk has been used to assay the mammary transcriptome non-invasively, this assay has not been adequately validated in primates. Thus, the objectives of the current study were to assess the suitability of lactating rhesus macaques as a model for lactating humans and to determine whether RNA extracted from milk fractions is representative of RNA extracted from mammary tissue for the purpose of studying the transcriptome of milk-producing cells.

Results: We confirmed that macaque milk contains cytoplasmic crescents and that ample high-quality RNA can be obtained for sequencing. Using RNA sequencing, RNA extracted from macaque milk fat and milk cell fractions more accurately represented RNA from mammary epithelial cells (cells that produce milk) than did RNA from whole mammary tissue. Mammary epithelium-specific transcripts were more abundant in macaque milk fat, whereas adipose or stroma-specific transcripts were more abundant in mammary tissue. Functional analyses confirmed the validity of milk as a source of RNA from milk-producing mammary epithelial cells.

Conclusions: RNA extracted from the milk fat during lactation accurately portrayed the RNA profile of milk-producing mammary epithelial cells in a non-human primate. However, this sample type clearly requires protocols that minimize RNA degradation. Overall, we validated the use of RNA extracted from human and macaque milk and provided evidence to support the use of lactating macaques as a model for human lactation.
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http://dx.doi.org/10.1186/1471-2164-14-872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3871720PMC
December 2013
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