BioTechnology Institute

Bacteria able to transfer electrons to conductive surfaces are of interest as catalysts in microbial fuel cells, as well as in bioprocessing, bioremediation, and corrosion. New procedures for immobilization of Geobacter sulfurreducens on graphite electrodes are described that allow routine, repeatable electrochemical analysis of cell–electrode interactions. Immediately after immobilizing G. sulfurreducens on electrodes, electrical current was obtained without addition of exogenous electron shuttles or electroactive polymers. Voltammetry and impedance analysis of pectin-immobilized bacteria transferring electrons to electrode surfaces could also be performed. Cyclic voltammetry of immobilized cells revealed voltage-dependent catalytic current similar to what is commonly observed with adsorbed enzymes, with catalytic waves centered at −0.15 V (vs. SHE). Electrodes maintained at +0.25 V (vs. SHE) initially produced 0.52 A/m2 in the presence of acetate as the electron donor. Electrical Impedance Spectroscopy of coatings was also consistent with a catalytic mechanism, controlled by charge transfer rate. When electrodes were maintained at an oxidizing potential for 24 h, electron transfer to electrodes increased to 1.75 A/m2. These observations of electron transfer by pectin-entrapped G. sulfurreducens appear to reflect native mechanisms used for respiration. The ability of washed G. sulfurreducens cells to immediately produce electrical current was consistent with the external surface of this bacterium possessing a pathway linking oxidative metabolism to extracellular electron transfer. This electrochemical activity of pectin-immobilized bacteria illustrates a strategy for preparation of catalytic electrodes and study of Geobacter under defined conditions. Biotechnol. Bioeng. 2008;99: 1065–1073. © 2007 Wiley Periodicals, Inc.

Background: Human milk contains a diverse population of bacteria that likely influences colonization of the infant gastrointestinal tract. Recent studies, however, have been limited to characterization of this microbial community by 16S rRNA analysis. In the present study, a metagenomic approach using Illumina sequencing of a pooled milk sample (ten donors) was employed to determine the genera of bacteria and the types of bacterial open reading frames in human milk that may influence bacterial establishment and stability in this primal food matrix. The human milk metagenome was also compared to that of breast-fed and formula-fed infants' feces (n = 5, each) and mothers' feces (n = 3) at the phylum level and at a functional level using open reading frame abundance. Additionally, immune-modulatory bacterial-DNA motifs were also searched for within human milk.

Mother's milk represents a foundational step in the proper development of newborn immunity. This is achieved, in part, through the action of numerous regulatory proteins such as soluble cluster of differentiation 14 (sCD14) found in significant quantities in human milk (ϳ25-50 g/mL). In adults, CD14 stimulates cytokine production in response to lipopolysaccharide (LPS), the major lipid component found in the outer membrane of Gram-negative bacteria. However, the fate and function of sCD14 in the neonatal gastrointestinal (GI) tract are unknown and may function differently from adults. Therefore, we administered human sCD14 to experimental animals and observed that it persisted in the upper GI tract after feeding. In our search for potential proteolytic protectants, immunoprecipitation of sCD14 from human milk revealed a 15-kD novel protein that copurified with sCD14. Mass spectrometry analysis of the protein identified alpha-lactalbumin. CD14 was also identified by immunoblot after immunoprecipitation of alpha-lactalbumin from milk. In vitro digestion assays revealed that purified alphalactalbumin decreases the proteolytic degradation of human milk derived sCD14 in vitro, suggesting a mechanism by which this key LPS receptor may remain functional in the neonate gut. (Pediatr Res 68: 490-493, 2010)

Transgenic mouse mutation detection systems allow investigation of the origins and mechanisms of mutation associated with exogenous and endogenous mutagen exposures in individual tissues and cell types. In the past, selection assays for transgenic mutants have been contaminated with nonmurine-derived mutations and assay validation is critical to ensure murine in vivo origins of mutations. This is critical in studies of spontaneous mutations and extrapolation to endogenous mammalian genes. Herein, we provide one measure of the contribution of Escherichia coli (E. coli)-derived mutations to the Big Blue® cII transgene mutant selection assay. We report the first direct evidence of an E. coli-derived cII mutation identified among mutations recovered in the cII selective assay. An E. coli transposable 5 (Tn5) element IS50R inverted repeat (1,534 bp) was identified at base pair 414 in the cII transgene and the insertion generated a 9 bp target site duplication typical of this type of transposition. The bacterial transposition occurred only once in the assay of 25 × 106 plaque forming units and sequencing of 1,177 cII mutants. The observed frequency of this type of mutation is 4 × 10−8 in retrieved λ phage and 8.5 × 10−4 in harvested cII mutants and thus a very rare occurrence in typical analyses of spontaneous in vivo mutations. Given that the frequency of transposition is equal to, or an order of magnitude higher, than the frequency of point mutations in E. coli, this article provides excellent validation for the murine origins of mutations detected using the cII mutant selection assay. Environ. Mol. Mutagen. 2010. © 2010 Wiley-Liss, Inc.

Applications of gene technology in agriculture, the environment and human health fields are reviewed. This case study of the intricate historical details of the development of Bt crops like cotton and rice unveils essential elements of productive funding schemes and effective multinational collaborations. Gene technology applied to pest resistance traits in global cotton is analyzed using nation-specific data from India to demonstrate ‘ricochet’ results: Regulatory approval for one crop catalyzes an ‘Enhancer Effect’ for promoting more research funding and more competitive results for other crops-in-waiting, namely rice. Just as cotton commerce promoted philanthropy in unpredictable situations like the Kreenholm dynasty of Ludwig Knoop, research budgets for pesticide and biocide technology have yielded intended effects, but several surprising unintended effects as well. Finally, the case is made for greater control of gene flow and identity preserve issues in plant biotechnology research by invoking Appellation d’Origine Contrôlée for Bt genes.

Soluble CD14 (sCD14) is a pattern recognition receptor and Toll-like co-receptor observed in human milk (5-26 g/mL) and other bodily fluids such as blood (3 g/mL). The most well defined role of sCD14 is to recognize lipopolysaccharide of Gram-negative bacteria and signal an immune response through Tolllike receptor 4 (TLR4). Previous research has shown ingested sCD14 to transfer from the gastrointestinal tract and into the blood stream in neonatal rats. The contribution of human milk sCD14 to circulating levels in the infant and the functionality of the protein, however, remained unknown. Using CD14 −/− mouse pups fostered to wild type (WT) mothers expressing sCD14 in their milk, we show herein that ingestion of sCD14 resulted in blood sCD14 levels up 0.16 ± 0.09 g/mL. This represents almost onethird (26.7%) of the circulating sCD14 observed in WT pups fostered to WT mothers (0.60 ± 0.14 g/mL). We also demonstrate that ingested-sCD14 transferred to the blood remains functional in its ability to recognize lipopolysaccharide as demonstrated by a significant increase in immune response (IL-6 and TNF-␣) in CD14 −/− pups fostered to WT mothers in comparison to control animals (P = 0.002 and P = 0.007, respectively). Using human intestinal cells (Caco-2), we also observed a significant decrease in sCD14 transcytosis when TLR4 was knocked down (P < 0.001), suggesting sCD14 transfer involves TLR4. The bioavailability of human milk sCD14 established in this report confirms the importance of human milk proteins for the infant and demonstrates the need to improve infant formulas which are lacking in immune proteins such as sCD14.

The primate gastrointestinal tract is home to trillions of bacteria, whose composition is associated with numerous metabolic, auto-immune, and infectious human diseases. Although there is increasing evidence that modern and Westernized societies are associated with dramatic loss of natural human gut microbiome diversity, the causes and consequences of such loss are challenging to study. Here we use nonhuman primates (NHPs) as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. Using 16S rRNA gene sequenc-ing in two model NHP species, we show that although different primate species have distinctive signature microbiota in the wild, in captivity they lose their native microbes and become colonized with Prevotella and Bacteroides, the dominant genera in the modern human gut microbiome. We confirm that captive individuals from eight other NHP species in a different zoo show the same pattern of convergence, and that semicaptive primates housed in a sanctuary represent an intermediate microbiome state between wild and captive. Using deep shotgun sequencing, chemical dietary analysis, and chloroplast relative abundance, we show that decreasing dietary fiber and plant content are associated with the captive primate microbiome. Finally, in a meta-analysis including published human data, we show that captivity has a parallel effect on the NHP gut microbiome to that of Westernization in humans. These results demonstrate that captivity and lifestyle disruption cause primates to lose native microbiota and converge along an axis toward the modern human microbiome.

Background: Bacteremia, or bloodstream infection (BSI), is a leading cause of death among patients with certain types of cancer. A previous study reported that intestinal domination, defined as occupation of at least 30 % of the microbiota by a single bacterial taxon, is associated with BSI in patients undergoing allo-HSCT. However, the impact of the intestinal microbiome before treatment initiation on the risk of subsequent BSI remains unclear. Our objective was to characterize the fecal microbiome collected before treatment to identify microbes that predict the risk of BSI. Methods: We sampled 28 patients with non-Hodgkin lymphoma undergoing allogeneic hematopoietic stem cell transplantation (HSCT) prior to administration of chemotherapy and characterized 16S ribosomal RNA genes using high-throughput DNA sequencing. We quantified bacterial taxa and used techniques from machine learning to identify microbial biomarkers that predicted subsequent BSI.

The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research, including longitudinal studies of mother–infant pairs while monitoring long-term health outcomes, further exploration of bacterium–fungus interactions, and improved methods and databases for mycobiome quantitation.

It has previously been shown that domestic dogs and their household owners share bacterial populations, and that sharing of bacteria between humans is facilitated through the presence of dogs in the household. However, less is known regarding the bacterial communities of dogs, how these communities vary by location and over time, and how cohabitation of dogs themselves influences their bacterial community. Furthermore, the effects of factors such as breed, hair coat length, sex, shedding, and age on the canine skin microbiome is unknown. This study sampled the skin bacterial communities of 40 dogs belonging to 20 households longitudinally across three seasons (spring, summer, and winter). Significant differences in bacterial community structure between samples were identified when stratified by season, but not by dog sex, age, breed, hair type, or skin site. Cohabitating dogs were more likely to share bacteria of the skin than non-cohabitating dogs. Similar to human bacterial microbiomes, dogs' microbiomes were more similar to their own microbiomes over time than to microbiomes of other individuals. Dogs sampled during the same season were also more similar to each other than to dogs from different seasons, irrespective of household. However, there were very few core operational taxonomic units (OTUs) identified across all dogs sampled. Taxonomic classification revealed Propionibacterium acnes and Haemophilus sp. as key members of the dog skin bacterial community, along with Corynebacterium sp. and Staphylococcus epidermidis. This study shows that the skin bacterial community structure of dogs is highly individualized, but can be shared among dogs through cohabitation.

With the advent of next-generation sequencing and microbial community characterization, we are beginning to understand the key factors that shape early-life microbial colonization and associated health outcomes. Studies characterizing infant microbial colonization have focused mostly on bacteria in the microbiome and have largely neglected fungi (the mycobiome), despite their relevance to muco-sal infections in healthy infants. In this pilot study, we characterized the skin, oral, and anal mycobiomes of infants over the first month of life (n 17) and the anal and vaginal mycobiomes of mothers (n 16) by internal transcribed spacer 2 (ITS2) amplicon sequencing. We found that infant mycobiomes differed by body site, with the infant mycobiomes at the anal sites being different from those at the skin and oral sites. The relative abundances of body site-specific taxa differed by birth mode, with significantly more Candida albicans fungi present on the skin of vaginally born infants on day 30 and significantly more Candida orthopsilosis fungi present in the oral cavity of caesarean section-born infants throughout the first month of life. We found the mycobiomes within individual infants to be variable over the first month of life, and vaginal birth did not result in infant mycobiomes that were more similar to the mother's vaginal mycobiome. Therefore, although vertical transmission of specific fungal isolates from mother to infant has been reported, it is likely that other sources (environment, other caregivers) also contribute to early-life mycobiome establishment. Thus, future longitudinal studies of mycobiome and bacterial micro-biome codevelopment, with dense sampling from birth to beyond the first month of life, are warranted. IMPORTANCE Humans are colonized by diverse fungi (mycobiome), which have received much less study to date than colonizing bacteria. We know very little about the succession of fungal colonization in early life and whether it may relate to long-term health. To better understand fungal colonization and its sources, we studied the skin, oral, and anal mycobiomes of healthy term infants and the vaginal and anal mycobiomes of their mothers. Generally, infants were colonized by few fungal taxa, and fungal alpha diversity did not increase over the first month of life. There was no clear community maturation over the first month of life, regardless of body site. Key body-site-specific taxa, but not overall fungal community structures, were impacted by birth mode. Thus, additional studies to characterize mycobiome acquisition and succession throughout early life are needed to form a foundation for research into the relationship between mycobiome development and human disease.

Salmonella enterica serovar Typhimurium continues to be a major cause of foodborne illness worldwide and pork can serve as a source of infection. Co-infection of S. enterica with Lawsonia intracellularis, a common intestinal pathogen of swine, has been found as risk factor for increased S. enterica shedding. The objective of this study was to investigate if vaccination against L. intracellularis could lead to decreased S. Typhimurium shedding. To test this hypothesis, pigs were challenged with either S. Typhimurium or S. Typhimurium and L. intracellularis, with and without L. intracellularis vaccination (n = 9 per group). A non-challenged group served as a negative control. Vaccination decreased the shedding of S. Typhimurium in co-infected animals by 2.12 log 10 organisms per gram of feces at 7 days post infection. Analysis of the microbiome showed that vaccination led to changes in the abundance of Clostridium species, including Clostridium butyricum, in addition to other compositional changes that may explain the protection mediated against S. Typhimurium. These results indicate that vaccination against L. intracellularis in co-infected herds may provide a new tool to increase food safety by helping to prevent S. enterica without the need for antibiotics. Salmonella enterica is a leading cause of foodborne illness worldwide 1. In the United States, the Centers for Disease Control and Prevention has estimated that S. enterica is responsible for over 1 million cases of foodborne illness per year, and is the leading cause of death due to foodborne illnesses 2. It has been estimated that the economic losses due to salmonellosis in the United States exceed $3 billion per year 3. Past studies have estimated that levels of human salmonellosis due to pork consumption vary; in the United States around 6% of outbreaks can be attributable to pork while in western European countries pork has been found to account for 44% of cases 4. Pigs frequently carry S. enterica, and efforts in the United States to reduce the incidence of salmonellosis have mainly remained ineffective. The prevalence of S. enterica in pigs is approximately 52.6% 5 and the incidence of salmonellosis in humans has not been reduced appreciably since 1996 6. Some believe that control of S. enterica in swine may not be possible using current technologies, there are many sources of infection including feed, the environment, and carrier animals 7,8. Factors such as stresses associated with transportation to slaughter plants, pathogen transmission during the comingling of pigs during lairage at processing plants, and introduction of new gilts into breeding herds contribute to increased shedding and transmission of S. enterica during pork production 9–11. However, these are not particularly amenable targets for developing improved control strategies. The source of S. enterica that contaminates pork products are the animals themselves 10 and novel intervention strategies are needed. L. intracellularis is a common porcine intestinal pathogen and is prevalent in pig production sites worldwide, with prevalence ranging from 48 to 100% in different swine producing countries 12. In the United States, it has been estimated that L. intracellularis is present in more than 90% of swine farms 13. L. intracellularis causes porcine

Fecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection, but has been less studied as a means to restore microbiome diversity and composition following antibiotic or chemotherapy treatments. The purpose of our study was to assess the efficacy of FMT to reverse antibiotic-and chemotherapy-induced gut dysbiosis in a mouse model. C57BL/6J mice were treated with ampicillin for 1 week and/or received a single intraperitoneal injection of 5-Fluorouracil. Fresh stool was collected and analyzed using shotgun metagenomics and the Illumina sequencing platform. Ampicillin caused a significant and immediate decrease in bacterial species richness and diversity that persisted for one week. In mice that received FMT, disruption of the intestinal microbiota was reversed immediately. Antibiotic and chemotherapy administration caused significant alteration in species distribution, including a decrease in the relative proportions of Clostridium scindens and Faecalibacterium prausnitzii, and an increase in known pathogenic species. In mice receiving FMT, we observed a significant increase in species known to exhibit anti-inflammatory properties. Moreover, chemotherapy led to a critical decrease in key 'health-promoting' species and to an altered functional profile, especially when chemotherapy was administered in tandem with antibiotics, and that FMT can ameliorate these effects. Cancer patients, especially those with hematological malignancies, receive high doses of chemotherapeutic agents that often cause for gastrointestinal mucositis 1. This side effect can enable bacterial translocation leading to bloodstream infection (BSI), a major cause of morbidity and mortality in cancer patients 2. In previous studies, the incidence of BSI was reported to be 20% to 60% in patients receiving high dose chemotherapy, and sepsis-associated mortality ranged from 9% to 31% 3–5. It was previously reported that the intestinal microbiota are drastically altered following chemotherapy, and that intestinal microbiota composition in pretreatment individuals can be used to predict the onset of subsequent bacteremia 6,7. These authors reported that several taxa, including Barnesiellaceae, Christensenella and Faecalibacterium, were less abundant in patients who developed a subsequent BSI. It was postulated that these strains could play a protective role against BSI. Myelosuppresive chemotherapy and some malignancies themselves lead to immunosuppression and to increased susceptibility to bacterial infections. Thus, prophylactic and empirical antibiotics are commonly used to reduce morbidity and mortality 4,8. Antibiotic treatments also adversely affect the gut microbiota and enable colonization with multidrug-resistant bacteria 9. Fecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection (rCDI) with clinical success rates >90% 10. Intestinal microbiota composition following FMT is restored

Red-shanked doucs (Pygathrix nemaeus) are endangered, foregut-fermenting colobine primates which are difficult to maintain in captivity. There are critical gaps in our understanding of their natural lifestyle, including dietary habits such as consumption of leaves, unripe fruit, flowers, seeds, and other plant parts. There is also a lack of understanding of enteric adaptations, including their unique microflora. To address these knowledge gaps, we used the douc as a model to study relationships between gastrointestinal microbial community structure and lifestyle. We analyzed published fecal samples as well as detailed dietary history from doucs with four distinct lifestyles (wild, semi-wild, semi-captive, and captive) and determined gastrointestinal bacterial microbiome composition using 16S rRNA sequencing. A clear gradient of microbiome composition was revealed along an axis of natural lifestyle disruption, including significant associations with diet, biodiversity, and microbial function. We also identified potential microbial biomarkers of douc dysbiosis, including Bacteroides and Prevotella, which may be related to health. Our results suggest a gradient-like shift in captivity causes an attendant shift to severe gut dysbiosis, thereby resulting in gastrointestinal issues. The primate gastrointestinal (GI) tract is home to trillions of bacteria that play major roles in digestion and metabolism, immune system development, pathogen resistance, and other important aspects of host health and behavior 1–4. While there has been substantial progress in understanding the role microbial communities play in human health and disease 1–3 , as well as numerous microbiome studies in non-primate animal models such as mice 5–9 , somewhat less attention has been given to host-associated microbiomes and lifestyle, including diet, in nonhuman primates (NHPs). Developing a better understanding of the link between primate microbial Published: xx xx xxxx OPEN