Fecal Bacterial Microbiota Research Articles

Bacterial fecal microbiota is only minimally affected by a standardized weight loss plan in obese cats

BackgroundResearch in humans and mice suggests that obesity influences the abundance and diversity of gastrointestinal (GI) microbiota, and that an “obese microbiome” influences energy metabolism and fat storage in the host. Microbiota membership and composition have been previously assessed in healthy cats. However, research investigating the effects of obesity and weight loss on the cat’s fecal microbiota is limited. Therefore, this study’s objective was to evaluate differences in fecal microbial abundance and biodiversity, as well as serum cobalamin and folate concentrations in obese cats, before and after weight loss, and compare to lean cats.Fourteen lean and 17 obese healthy client-owned cats were fed a veterinary therapeutic weight loss food at maintenance energy requirement for 4 weeks. At the end of week 4, lean cats finished the study, whereas obese cats continued with a 10-week weight loss period on the same food, fed at individually-tailored weight loss energy requirements. Body weight and body condition score were recorded every 2 weeks throughout the study. At the end of each period, a fecal sample and food-consumption records were obtained from the owners, and serum cobalamin and folate concentrations were analysed. DNA was extracted from fecal samples, polymerase chain reaction (PCR) was performed, and products were sequenced using next-generation sequencing (Illumina MiSeq).ResultsNo significant differences in the relative abundance of taxa and in biodiversity indices were observed between cats in either group (P > 0.05 for all tests). Nevertheless, some significantly enriched taxa, mainly belonging to Firmicutes, were noted in linear discriminant analysis effect size test in obese cats before weight loss compared to lean cats. Serum cobalamin concentrations were significantly higher in lean compared to obese cats both before and after weight loss. Serum folate concentrations were higher in obese cats before weight loss compared to after.ConclusionsThe association between feline obesity and the fecal bacterial microbiota was demonstrated in enriched taxa in obese cats compared to lean cats, which may be related to enhanced efficiency of energy-harvesting. However, in obese cats, the fecal microbial abundance and biodiversity were only minimally affected during the early phase of a standardized weight loss plan.

The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea.

Background and aimsFecal microbial transplantation (FMT), a treatment for certain gastrointestinal conditions associated with dysbiosis in people, is also empirically employed in horses with colitis. This study used microbiota high-throughput sequencing to compare the fecal microbial profile of healthy horses to that of geriatric microbial transplant recipients experiencing diarrhea and tested whether FMT restores microbiota diversity.MethodsTo evaluate the effect of environment and donor characteristics on the intestinal microbiota, fecal samples were collected per rectum from 15 healthy young-adult (2–12 years) and 15 geriatric (≥20 years) horses. Additionally, FMT was performed for 3 consecutive days in 5 geriatric horses with diarrhea using feces from the same healthy donor. Fecal samples were collected from both donor and recipient prior to each FMT and from recipients 24 hours following the last FMT. The profile of the fecal bacterial microbiota was compared using 16S amplicon sequencing.Results and conclusionsIn contrast to diet and farm location, age did not significantly affect the healthy equine fecal microbiota, indicating that both healthy geriatric and young-adult horses may serve as FMT donors. The fecal microbiota of horses with diarrhea was significantly more variable in terms of β-diversity than that of healthy horses. An inverse correlation between diarrhea score and relative abundance of Verrucomicrobia was identified in surviving FMT recipients. At study completion, the fecal microbiota of horses which responded to FMT had a higher α-diversity than prior to treatment and was phylogenetically more similar to that of the donor.

Chronic diarrhea, bile acids, and Clostridia.

Excessive fecal bile acid (BA) loss causes symptoms in a large proportion of people diagnosed with irritable bowel syndrome with diarrhea, a common functional bowel disorder. This BA diarrhea (BAD) results from increased hepatic synthesis of BAs, with impaired negative feedback regulation by the ileal hormone fibroblast growth factor 19 (FGF19). In this issue of the JCI, Zhao et al. investigated BA metabolism, including fecal BAs, serum BAs, and FGF19, in patients and controls. They identified associations between fecal bacterial BA metabolism and specific microbiota, especially Clostridium scindens. These findings have been tested in a mouse model using microbiota transplants and antibiotic treatment. This group of organisms has potential as a biomarker for BAD and to be a target for therapy.

Effect of Parkinson\u2019s disease and related medications on the composition of the fecal bacterial microbiota

Parkinson’s disease (PD) is one of the most common neurodegenerative disorders. PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS). Such alterations and functional gastrointestinal deficits often occur years before the classical clinical symptoms of PD appear. Until now, only little is known about PD-associated changes in gut microbiota composition and their potential implication in PD development. In order to increase knowledge in this field, fecal samples of 34 PD patients and 25 healthy, age-matched control persons were investigated. Here, the V4 and V5 hypervariable region of bacterial 16S rRNA genes was PCR-amplified and sequenced using an Ion Torrent PGM platform. Within the PD group, we observed a relative decrease in bacterial taxa which are linked to health-promoting, anti-inflammatory, neuroprotective or other beneficial effects on the epithelial barrier, such as Faecalibacterium and Fusicatenibacter. Both taxa were lowered in PD patients with elevated levels of the fecal inflammation marker calprotectin. In addition, we observed an increase in shares of the Clostridiales family XI and their affiliated members in these samples. Finally, we found that the relative abundances of the bacterial genera Peptoniphilus, Finegoldia, Faecalibacterium Fusicatenibacter, Anaerococcus, Bifidobacterium, Enterococcus, and Ruminococcus were significantly influenced by medication with L-dopa and entacapone, respectively. Our data confirm previously reported effects of COMT inhibitors on the fecal microbiota of PD patients and suggest a possible effect of L-dopa medication on the relative abundance of several bacterial genera.

Changes of intestinal bacterial microbiota in coronary heart disease complicated with nonalcoholic fatty liver disease

BackgroundPrevious study reported that patients who suffered coronary heart disease (CHD) complicated with non-alcoholic fatty liver disease (NAFLD) had worse cardiac function and clinical outcomes than patients with CHD only. Notably, the mechanism is still unclear. This study aimed to investigate the changes and roles of intestinal bacterial microbiota in CHD-NAFLD patients.Methods and resultsPeople were recruited and divided into three groups, including CHD patients (without NAFLD), CHD-NAFLD patients and healthy controls (HCs). Each group contained 24 people. Fecal samples and clinical information were carefully collected. The Illumina sequencing of 16S rRNA was applied to profile the overall structure of the fecal bacterial microbiota and the characteristics of the bacterial microbiota based on the Operational Taxonomic Units. In clinical information, the CHD-NAFLD patients showed an increase in BMI, uric acid and triglyceride. There was a significant reduction in the abundance of Parabacteroides and Collinsella in overall CHD patients (including CHD-NAFLD and CHD patients). The intestinal bacterial microbiota in CHD-NAFLD patients showed an increase in the abundance of Copococcus and Veillonella, and a reduction in the abundance of Parabacteroides, Bacteroides fragilis, Ruminococcus gnavus, Bacteroides dorei, and Bifidobacterium longum subsp infantis. Among them, the abundance of Ruminococcus gnavus and Bacteroides dorei was significantly lower than that in CHD patients. Additionally, BMI positively correlated with the abundance of Copococcus and negatively correlated with the abundance of Bifidobacterium longum subsp infantis. The abundance of Veillonella positively correlated with AST. The abundance of Bacteroides dorei negatively correlated with ALT and AST. It indicates that the abundance of intestinal microbiota was related to the changes in clinical indexes.ConclusionsChanges of intestinal bacterial microbiota in CHD-NAFLD patients may be important factors affecting the degree of metabolic disorder, which may be one of the important reasons for the worse clinical outcome and disease progression in CHD-NAFLD patients than in CHD patients.

Anthocyanin-enriched bilberry extract attenuates glycaemic response in overweight volunteers without changes in insulin

Abstract This study investigated the effect of a three week supplementation of bilberry extract on glucose metabolism. Overweight volunteers (n = 16; BMI 31) were given three capsules of either 0.47 g bilberry extract (36% (w/w) anthocyanins) or placebo per day for three weeks in a double blinded cross over intervention. The ingestion of the bilberry extract decreased the OGTT AUCi for glucose (20%; p = 0.008) but not for insulin compared with the placebo. There was no change in anti-inflammatory markers (hsCRP, MCP-1, leptin), vascular health markers (Apo A1, sVCAM-1, sICAM-1), reducing potential/ radical scavenging capacity or faecal bacterial microbiota. In vitro studies showed that the bilberry extract decreased α-amylase activity (p This study demonstrates that the ingestion of a bilberry extract over a three week intervention period reduces postprandial glycaemia without changes in insulin. This is probably due to reduced rates of carbohydrate digestion and/or absorption.

The composition and stability of the faecal microbiota of Merino sheep.

To determine the composition and temporal stability of the gut (faecal) microbiota of sheep (Ovis aries). Microbial population dynamics was conducted using ARISA (28 sheep) and 16S rRNA sequencing (11 sheep). Firmicutes and Bacteroidetes were the predominant bacterial phyla, constituting ~80% of the total population. The core faecal bacterial microbiota of sheep consisted of 67 of 136 detected families and 91 of 215 detected species. Predominant microbial taxa included Ruminococcaceae, unassigned families in Bacteroidales and Clostridiales, Verrucomicrobiaceae and Paraprevotellaceae. Diversity indices and core microbiota composition demonstrated the stability of the core microbiota over 2-4weeks. The core microbiota remained similar over ~5months. Temporal stability of the sheep microbiota is high over 2-4weeks in the absence of experimental variables. The core microbiota of Merino sheep shares taxa found in other breeds of sheep and other ruminants. Numerous studies seek to investigate the impact of experimental variables on gut microbiota composition. To do so, knowledge of the innate stability (or instability) of the microbiota over an experimental time course is required, independent of other variables. We have demonstrated high stability of the gut microbiota in sheep over 3-4weeks, with moderate stability over ~5months.

First insights into the fecal bacterial microbiota of the black–tailed prairie dog (Cynomys ludovicianus) in Janos, Mexico

espanolLas bacterias intestinales son un indicador importante de la salud de su hospedero y la incorporacion de una evaluacion periodica de la composicion taxonomica de estos microorganismos en los planes de gestion y conservacion puede ser una herramienta valiosa para detectar cambios que puedan poner en peligro la supervivencia de las poblaciones amenazadas. En este estudio describimos la diversidad y abundancia de las bacterias fecales de una especie amenazada, el perrito de la pradera de cola negra (Cynomys ludovicianus), en la Reserva de la Biosfera de Janos, en Chihuahua, Mexico. Se analizaron muestras fecales mediante secuenciacion masiva de siguiente generacion y se amplifico la region V3–V4 del gen que codifica el ARNr 16S utilizando la tecnologia Illumina. Los resultados se analizaron con QIIME a partir de la referencia EzBioCloud. Se identificaron 12 filos, 22 clases, 33 ordenes, 54 familias y 263 generos. Los filos Firmicutes y Bacteroidetes, que fueron los grupos mas abundantes, se asocian con comunidades intestinales saludables y una alta eficiencia en la dieta energetica. La mayoria de los generos bacterianos detectados en este estudio para C. ludovicianus no son patogenos y se encuentran habitualmente en las heces de mamiferos. Algunas de las otras bacterias estan asociadas al suelo, el agua y las plantas, posiblemente en relacion con el habitat del perrito de las praderas de cola negra. Este es el primer estudio que reporta las bacterias fecales de C. ludovicianus en Mexico y que proporciona un punto de referencia para determinar la salud de esta especie con vistas a utilizar esta informacion en estrategias de conservacion a largo plazo. EnglishIntestinal bacteria are an important indicator of the health of their host. Incorporating periodic assessment of the taxonomic composition of these microorganisms into management and conservation plans can be a valuable tool to detect changes that may jeopardize the survival of threatened populations. Here we describe the diversity and abundance of fecal bacteria for the black–tailed prairie dog (Cynomys ludovicianus), a threatened species, in the Janos Biosphere Reserve, Chihuahua, Mexico. We analyzed fecal samples through next generation massive sequencing and amplified the V3–V4 region of the 16S rRNA gene using Illumina technology. The results were analyzed with QIIME based on the EzBioCloud reference. We identified 12 phyla, 22 classes, 33 orders, 54 families and 263 genera. The phyla Firmicutes and Bacteroidetes were the most abundant groups and are associated with healthy intestinal communities and high efficiency in the energy diet. Most of the bacterial genera reported here for C. ludovicianus are not pathogenic and are normally found in mammalian feces. Some of the other bacteria are associated with soil, water and plants, possibly in relation to the habitat of the black– tailed prairie dog. This is the first study to report the fecal bacteria of C. ludovicianus in Mexico and it provides a baseline for determining this species' health for use in long–term conservation strategies.

Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns.

Blastocystis is the most prevalent protist of the human intestine, colonizing approximately 20% of the North American population and up to 100% in some nonindustrialized settings. Blastocystis is associated with gastrointestinal and systemic disease but can also be an asymptomatic colonizer in large populations. While recent findings in humans have shown bacterial microbiota changes associated with this protist, it is unknown whether these occur due to the presence of Blastocystis or as a result of inflammation. To explore this, we evaluated the fecal bacterial and eukaryotic microbiota in 156 asymptomatic adult subjects from a rural population in Xoxocotla, Mexico. Colonization with Blastocystis was strongly associated with an increase in bacterial alpha diversity and broad changes in beta diversity and with more discrete changes to the microbial eukaryome. More than 230 operational taxonomic units (OTUs), including those of dominant species Prevotella copri and Ruminococcus bromii, were differentially abundant in Blastocystis-colonized individuals. Large functional changes accompanied these observations, with differential abundances of 202 (out of 266) predicted metabolic pathways (PICRUSt), as well as lower fecal concentrations of acetate, butyrate, and propionate in colonized individuals. Fecal calprotectin was markedly decreased in association with Blastocystis colonization, suggesting that this ecological shift induces subclinical immune consequences to the asymptomatic host. This work is the first to show a direct association between the presence of Blastocystis and shifts in the gut bacterial and eukaryotic microbiome in the absence of gastrointestinal disease or inflammation. These results prompt further investigation of the role Blastocystis and other eukaryotes play within the human microbiome. IMPORTANCE Given the results of our study and other reports of the effects of the most common human gut protist on the diversity and composition of the bacterial microbiome, Blastocystis and, possibly, other gut protists should be studied as ecosystem engineers that drive community diversity and composition.

Fecal Bacteriome and Mycobiome in Bats with Diverse Diets in South China

Bats can be divided into frugivory, nectarivory, insectivory, and sanguivory based on their diets, and are therefore ideal wild animal models to study the relationship between diets and intestinal microflora. Early studies of bat gut bacteria showed that the diversity and structure of intestinal bacterial communities in bats are closely related to dietary changes. Worthy of note, intestinal microbes are composed of bacteria, fungi, protozoa, and archaea. Although the number of gut fungi is much lower than that of gut bacteria, they also play an important role in maintaining the host homeostasis. However, there are still few reports on the relationship between the gut mycobiota and the dietary habits of the host. In addition, bats have also been shown to naturally transmit pathogenic viruses and bacteria through their feces and saliva, but fungal infections from bat are less studied. Here, we used high-throughput sequencing of bacterial 16S and eukaryotic 18S rRNA genes in the V4 and V9 regions to characterize fecal bacterial and fungal microbiota in phytophagous and insectivorous bats in South China. The results show that the gut microbiota in bats were dominated by bacterial phyla Proteobacteria, Firmicutes, Tenericutes and Bacteroidetes, and fungal phyla Ascomycota and Basidiomycota. There was a significant difference in the diversity of bacterial and fungal microbiota between the groups, in addition to specific bacteria and fungi populations on each of them. Of note, the number of fungi in the feces of herbivorous bats is relatively higher. Most of these fungi are foodborne and are also pathogens of humans and other animals. Thus, bats are natural carriers of fungal pathogens. The current study expands the understanding of the bat gut bacterial and fungal mycobiota and provides further insight into the transmission of fungal pathogens.

The fecal bacterial microbiota of bats; Slovenia.

MethodsFecal samples were collected from 92 bats in Slovenia, consisting of 12 different species, and the bacterial microbiota was assessed via next generation sequencing of the 16S rRNA gene V4 region.ResultsSequences were assigned to 28 different phyla, but only Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria accounted for ≥1% of sequences. One phylum (Proteobacteria), one class (Gammaproteobacteria), three orders (Pseudomonadales, Lactobacillales, Bacillales), four families (Enterobacteriaceae, Pseudomonadaceae, Staphylococcaceae, Carnobacteriaceae), and five genera (Pseudomonas, Staphylococcus, Carnobacterium, an unclassified Enterobacteriaceae, Acinetobacter) accounted for 50% of sequences. There were no significant differences in the relative abundances of any phyla between bat species, but various differences were noted at lower taxonomic levels, such as Enterobacteriaceae (P = 0.007, most abundant in M. blythii), Pseudomonadaceae (P = 0.007, most abundant in Rhinolophus hipposideros) and Chlamydiaceae (P = 0.04, most abundant in Myotis myotis). There were significant differences in richness between species in both adults and juveniles/subadults, but there was no impact of sex on any alpha diversity index. When only adults are considered, there were significant differences in community membership between M. blythii and M. emarginatus (P = 0.011), and M. blythii and R. hipposideros (P = 0.004). There were also significant differences in community structure between M. blythii and M. emarginatus (P = 0.025), and M. blythii and R. hipposideros (P = 0.026). When adults of the four main species were compared, 14 OTUs were identified as differentially abundant using LEfSe. Only one difference was identified when comparing R. hipposideros adults and juvenile/subadults, with Klebsiella over-represented in the younger bats.ConclusionsBats have a complex and diverse microbiota with a high relative abundance of Proteobacteria. The relevance of this difference is unclear and requires further study. Differences in the microbiota were observed between bat species, perhaps reflecting different diets and environmental exposures.

Comparison Between the Fecal Bacterial Microbiota of Healthy and Diarrheic Captive Musk Deer

Diarrhea constitutes one of the most common diseases affecting the survival of captive musk deer and is usually caused by an imbalance in intestinal microbiota. Currently, research regarding the structure and function of intestinal microbiota in diarrheic musk deer is lacking. Therefore, in the present study, high-throughput 16S-rRNA gene sequencing was used to analyze the intestinal microbiota in feces of healthy captive musk deer (HMD) (n = 8) and musk deer with mild (MMD) (n = 8), and severe (n = 5) (SMD) diarrhea to compare the difference in intestinal microbiota of musk deer under various physiological conditions. The results showed that the diversity of HMD fecal microbiota was significantly higher than that of the two diarrhea samples. β Diversity results indicated that there were extremely significant differences in bacterial communities between the HMD sample and the MMD and SMD samples. However, no significant difference was found between the two diarrhea samples. LefSe analysis showed that the degree of intestinal physiological dysfunction in musk deer was correlated with the types of major pathogens. The main pathogen in the MMD group is Escherichia–Shigella, whereas Fusobacterium is the main pathogen in the SMD group. PICRUSt functional profile prediction indicated that the intestinal microbiota disorder could also lead to changes in the abundance of genes in metabolic pathways of the immune system. Altogether, this study provides a theoretical basis for the exploration of treatments for diarrhea in captive musk deer, which is of considerable significance to the implementation of the musk deer release into the wild program.

Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration

BackgroundGut microbiota may be altered in patients with cirrhosis, and may further change after administration of lactulose. We studied the composition of gut microbiota in patients with cirrhosis and assessed the effect on it of lactulose administration.MethodsStool specimens were collected from 35 patients with cirrhosis (male 26; median [range] age: 42 [29–65] years) and 18 healthy controls (male 14; 44.5 [24–67] years); 21 patients provided another specimen after lactulose administration for 55 [42–77] days. For each, a DNA library of V3 region of bacterial 16S ribosomal RNA was subjected to paired-end Illumina sequencing. Inter-specimen relationship was studied using principal co-ordinate analysis. Abundances of various bacterial taxa, and indices of alpha and beta diversity were compared, between patients and controls, and between specimens collected before and after lactulose.ResultsGut microbiota from cirrhosis patients and controls showed differential clustering, and microbiota from patients with cirrhosis had less marked alpha diversity. Abundances of dominant phyla (Bacteroidetes, Firmicutes and Proteobacteria) were similar. However, patients with cirrhosis had lower abundances of five phyla, namely Tenericutes, Cyanobacteria, Spirochaetes, Elusimicrobia and Lentisphaerae, and differences in abundances of several families and genera than in controls. Lactulose administration did not lead to any change in alpha and beta diversities, species richness and abundances of various bacterial taxa in gut microbiota.ConclusionsGut microbiota in cirrhosis differ from healthy persons and do not change following lactulose administration. The latter suggests that the effect of lactulose on hepatic encephalopathy may not be related to alteration in gut microbiota.

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life.

Few studies have analyzed the gut microbiota of child in unindustrialized countries, but none during the first month of life. Stool samples were collected from healthy newborns in hospitals of Gabon (n = 6) and Republic of the Congo (n = 9) at different time points during the first month of life: meconium, day 2 (D02), day 7 (D07) and day 28 (D28). In addition, one fecal sample was collected from each mother after delivery. Metagenomic sequencing was performed to determine the bacterial communities, and multiplex real-time PCR was used to detect the presence of seven enteric viruses (rotavirus a, adenovirus, norovirus I and II, sapovirus, astrovirus, enterovirus) in these samples. Bacterial diversity was high in the first days of life, and was dominated by the genus Prevotella. Then, it rapidly decreased and remained low up to D28 when the gut flora was composed almost exclusively of strictly anaerobic bacteria. Each infant’s fecal bacterial microbiota composition was significantly closer to that of their mother than to that of any other woman in the mothers’ group, suggesting an intrauterine, placental or amniotic fluid origin of such bacteria. Moreover, bacterial communities differed according to the delivery mode. Overall, the bacterial microbiota communities displayed a similar diversification and expansion in newborns within and between countries during the first four weeks of life. Moreover, six of the fifteen infants of this study harbored enteric viruses (rotavirus, enterovirus and adenovirus) in fecal samples, but never in the meconium. A maternal source for the viruses detected at D02 and D07 can be excluded because none of them was found also in the child’s mother. These findings improve our knowledge on the gut bacterial and viral communities of infants from two Sub-Saharan countries during their first month of life.

Comparison of the fecal bacterial microbiota of healthy and diarrheic foals at two and four weeks of life

BackgroundDiarrhea in foals affects up to 60% of foals during the first six months of life. The effect of diarrhea on the fecal bacterial microbiota in foals has not been investigated. Little is known on the fecal bacterial microbial richness and diversity of foals at a young age. The objective was to compare the fecal bacterial microbiota of healthy foals to foals with diarrhea at two and four weeks of life.MethodsFecal samples were collected from foals (n = 20) at 1–14 (T1) and 15–28 (T2) days of age and analyzed using high throughput sequencing. Differences in relative abundance of bacterial taxa, alpha diversity and beta diversity indices were assessed between age-matched foals with diarrhea (n = 9) and healthy foals (n = 11), and between time points.ResultsDifferences in microbial community composition based on time point and health status were observed on all taxonomic levels. Of 117 enriched species in healthy foals at T2, 50 (48%) were Lachnospiraceae or Ruminococcaceae. The Chao richness index was increased in healthy foals at T2 compared to T1 (p = 0.02). Foals with diarrhea had a significantly lower richness index than non-diarrheic foals at T2 (p = 0.04). Diarrhea had an inconsistent effect, while time point had a consistent effect on microbial community structure.ConclusionsPreventative and therapeutic measures for diarrhea should focus on maintaining bacterial microbiota richness. Lachnospiraceae and Ruminococcaceae were underrepresented in foals with diarrhea. These should be evaluated further as potential therapeutic options.

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves.

BackgroundNeonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population‐based studies of cattle have investigated how the microbiota is impacted during diarrhea.ObjectivesTo characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.MethodsFifteen diarrheic calves between the ages of 1 and 30 days and 15 age‐matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high‐throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).ResultsSignificant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.Clinical RelevanceThe fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.

Assessment of the Fecal Microbiota in Beef Calves.

BackgroundThere is increasing interest in the fecal microbiota, but study in calves has been limited.Hypothesis/ObjectivesTo evaluate the fecal microbiota of beef calves and cows on different farms, and to preliminarily explore the impact of antimicrobial exposure.AnimalsA total of 172 animals, 156 (91%) calves and 16 (9.3%) cows, were enrolled from 5 cow‐calf farms.MethodsThe fecal bacterial microbiota was assessed through sequencing of 16S rRNA gene (V4 region) amplicons.ResultsThere were significant differences in the relative abundances of numerous phyla between calves on different farms. Farms could be separated into 2 groups: 1 (farms B and C) dominated by Firmicutes and 1 (farms A, D, and E) with predominance of Proteobacteria and Actinobacteria. Richness (median 2,974 versus 1,477, P = .008), diversity (51.4 versus 29.1, P = .0029), and evenness (0.73 versus 0.68, P = .006) were higher in cows. Over‐represented operational taxonomic units (OTUs) in cows tended to be from the classes Bacilli and Bacteroidia, whereas Clostridia and Actinobacteria were most prominently over‐represented in calves. There were differences in community membership (P = .028) and structure (P = .029) in calves that had a history of antimicrobial exposure compared those that did not. Eight (89%) over‐represented OTUs in the untreated group were Firmicutes (7 from the order Clostridiales), compared to only 3 (38%) (2 Clostridiales) in the untreated group.Conclusions and Clinical ImportanceInterfarm variation should be investigated to determine the causes and potential implications for health and production. Antimicrobial exposure may have an impact on the fecal microbiota at individual and farm levels.

Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum

Understanding the interaction between the intestinal microbiota (microbiome) and enteric pathogens is of interest in the development of alternative treatments that do not rely on chemotherapy and do not lead to drug resistance. We undertook research in a rodent model of cryptosporidiosis to assess whether the bacterial gut microbiota is impacted by infection with the protozoan pathogen Cryptosporidium parvum. The profile of the faecal bacterial microbiota in infected and uninfected animals was compared using 16S amplicon sequencing. In four independent experiments, the intestinal microbiota of infected mice differed from that of uninfected animals, regardless of the C. parvum isolate used to infect mice. The use of replicated treatment groups demonstrated that microbiota divergence between treatments was driven by the infection and did not result from spontaneous changes in the intestinal ecosystem unrelated to the infection. Microbiota perturbation induced by C. parvum appeared to be reversible, as we observed a tendency for the phylogenetic distance between infected and uninfected mice to diminish after mice cleared the infection. As mice infected with C. parvum do not develop diarrhoea, these observations indicate that microbiota perturbation results from other mechanisms than an accelerated movement of gut content.

167 The Microbiome Signature of Autistic Children Is Characterized by Decreased Diversity and Dysbiosis

Background: Autism Spectrum Disorders (ASDs) are complex neuro-developmental disorders characterized by cognitive defects, social interaction skills impairments and communication, language and behavioral problems. A strong correlation between autism severity and GI symptoms, alterations of intestinal permeability (IP), presence of inflammation and intestinal dysbiosis has been described. It has recently been proposed that alterations of the intestinal microbiota could contribute to the development of ASDs. Recent studies demonstrated that autistic children with gastrointestinal symptoms show major fecal microbiota alterations. In this study we aimed to study the fecal candida and bacterial microbiota, their correlation to intestinal permeability, in autistic children compared to normal developing children, in order to provide rational basis to a possible specific therapeutic intervention in restoring gut microflora in ASDs. Material and Methods: We collected stool samples from 47 subjects with ASDs (40 boys and 7 girls, mean age 6.0 ± 2.8 yr), and 33 healthy children matched controls (24 boys and 9 girls, mean age 7.3 ± 3.1 yr). Search for Candida culture and biochemical identification of the colonies were performed by Sabouraud Dextrose Agar + Chloramphenicol + Gentamicin, Oxoid Products Microbiology and analized by ID 32 C (bioMerieux) system. In a subgroup of 12 ASDs subjects (8 boys and 4 girls, mean age 6.8 ± 2.9 ), and 16 healthy children matched controls (8 boys and 8 girls, mean age 7.3 ± 3.1 yr), total microbial DNA was extracted and 16S variable region V4 amplified by PCR. The results were analyzed by QIIME software. Intestinal Permeability (IP) was assessed with the lactulose/mannitol (LA/MA) test. Results: Compared to HC, ASDs samples presented an increased number of Proteobacteria combined with a reduction of Bacteroidetes and Actinobacteria. Microbial diversity was reduced in ASDs children, albeit they were more phylogenetically different. Interestingly, β-diversity analysis showed 2 distinct clouds in ASDs children, one dominated by E. Coli and the other with no clear domination. Candida spp was detected in the stools of 15 ASD children (31.9%) compared to controls (6.1%). Interestingly in ASDs, C. albicans was most frequently identified (9 out of 15 cases). Finally, IP resulted altered in 42.4% of ASDs compared to 22.7% of controls (p < 0.05). No correlation was detected between altered IP and either microbiome composition or candidosis. Conclusions: In this proof-of-concept study we establish that ASD children have a specific microbiome signature characterized by decreased diversity and quantitative representation of some specific phyla. Candida infestation, particularly C. albicans was more frequently detected in ASD children than controls.

Temporal analysis of the effect of extruded flaxseed on the swine gut microbiota.

Flaxseed is a rich source of α-linolenic acid, an essential ω-3 fatty acid reported to have beneficial health effects in humans. Feeding swine a diet supplemented with flaxseed has been found to enrich pork products with ω-3 fatty acids. However, the effect of flaxseed supplementation on the swine gut microbiota has not been assessed to date. The purpose of this study was to investigate if extruded flaxseed has any impact on the bacterial and archaeal microbiota in the feces of growing-finishing pigs over a 51-day period, using denaturing gradient gel electrophoresis (DGGE) and real-time PCR. Bacterial DGGE profile analysis revealed major temporal shifts in the bacterial microbiota with only minor ones related to diet. The archaeal microbiota was significantly less diverse than that of Bacteria. The majority of bacterial DGGE bands sequenced belonged to the Firmicutes phylum while the archaeal DGGE bands were found to consist of only 2 species, Methanobrevibacter smithii and Methanosphaera stadtmanae. The abundance of Bacteroidetes decreased significantly from day 0 to day 21 in all diet groups while the abundance of Firmicutes was relatively stable across all diet cohorts and sampling times. There was also no significant correlation between pig mass and the ratio of Firmicutes to Bacteroidetes. While the addition of extruded flaxseed to the feed of growing-finishing pigs was beneficial for improving ω-3 fatty acid content of pork, it had no detectable impact on the fecal bacterial and archaeal microbiota, suggesting that extruded flaxseed may be used to improve meat quality without adverse effect on the swine gut microbiota or animal performance.