An effective method for isolation of DNA from pig faeces and comparison of five different methods

Rigorous Process for Isolation of Gut-Derived Extracellular Vesicles (EVs) and the Effect on Latent HIV

The human gastrointestinal (GI) track host trillions of microorganisms that secrete molecules, including extracellular vesicles (EVs) and extracellular condensates (ECs) that may affect physiological and patho-physiological activities in the host. However, efficient protocols for the isolation of pure and functional GI-derived EVs|ECs is lacking. Here, we describe the use of high-resolution particle purification liquid chromatography (PPLC) gradient-bead-column integrated with polyvinylpolypyrrolidone (PVPP)-mediated extraction of impurities to isolate EVs from colonic content (ColEVs). PVPP facilitates the isolation of pure, non-toxic, and functionally active ColEVs that were internalized by cells and functionally activate HIV LTR promoter. ColEVs isolated without PVPP have a reductive effect on MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) without living cells, suggesting that ColEVs contain reductases capable of catalyzing the reduction of MTT to formazan. The assessment of the origin of ColEVs reveals that they are composed of both bacteria and host particles. This protocol requires ~12 h (5 h preprocessing, 7 h isolation) to complete and should be used to purify EVs from sources contaminated with microbial agents to improve rigor. This protocol provides a robust tool for researchers and clinicians investigating GI-derived EVs and the translational use of GI-derived EVs for diagnostic and therapeutic use. Additionally, GI-derived EVs may serve as a window into the pathogenesis of diseases.

Ancient DNA diffuses from human bones to cave stones

Recent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period

We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic analyses. The paleofeces were preserved in the underground salt mines of the UNESCO World Heritage site of Hallstatt in Austria. This allowed us to reconstruct the diet of the former population and gain insights into their ancient gut microbiome composition. Our dietary survey identified bran and glumes of different cereals as some of the most prevalent plant fragments. This highly fibrous, carbohydrate-rich diet was supplemented with proteins from broad beans and occasionally with fruits, nuts, or animal food products. Due to these traditional dietary habits, all ancient miners up to the Baroque period have gut microbiome structures akin to modern non-Westernized individuals whose diets are also mainly composed of unprocessed foods and fresh fruits and vegetables. This may indicate a shift in the gut community composition of modern Westernized populations due to quite recent dietary and lifestyle changes. When we extended our microbial survey to fungi present in the paleofeces, in one of the Iron Age samples, we observed a high abundance of Penicillium roqueforti and Saccharomyces cerevisiae DNA. Genome-wide analysis indicates that both fungi were involved in food fermentation and provides the first molecular evidence for blue cheese and beer consumption in Iron Age Europe.

Emodin Improves Intestinal Health and Immunity through Modulation of Gut Microbiota in Mice Infected by Pathogenic Escherichia coli O1

The effect of emodin on the intestinal mucosal barrier of a mouse E. coli O₁-induced diarrhea model was observed. Following successful establishment of a diarrhea model, the mice were treated with drugs for seven days. Intestinal lesions and the shape and the number of goblet cells were assessed via hematoxylin-eosin and periodic-acid-Schiff staining, while changes in inflammatory factors, ultrastructure of the small intestine, expression of MUC-2, and changes in the intestinal microbiota were analyzed via RT-PCR, electron microscopy, immunofluorescence, and 16S rRNA sequencing. Examination showed that emodin ameliorated pathological damage to the intestines of diarrheic mice. RT-PCR indicated that emodin reduced TNF-α, IL-β, IL-6, MPO, and COX-2 mRNA levels in duodenal tissues and increased the levels of sIgA and MUC-2 and the number of goblet cells. Microbiome analysis revealed that Escherichia coli O₁ reduced bacterial richness and altered the distribution pattern of bacterial communities at the phylum and order levels in cecum contents. Notably, pathogenic Clostridiales and Enterobacteriales were significantly increased in diarrheic mice. However, emodin reversed the trend. Thus, emodin protected against intestinal damage induced by E. coli O₁ and improved intestinal mucosal barrier function in mice by increasing the abundance of beneficial intestinal microbiota and inhibiting the abundance of harmful bacteria, thereby alleviating diarrhea.

DNA methylation profiling in mummified human remains from the eighteenth-century

Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we were able to detect characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions matched the fact that the specimen was lung tissue from a 28-year-old woman. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.

Seasonal and Age-Associated Pathogen Distribution in Newborn Calves with Diarrhea Admitted to ICU

Calf mortality constitutes a substantial loss for agriculture economy-based countries and is also a significant herd problem in developed countries. However, the occurrence and frequency of responsible gastro-intestinal (GI) pathogens in severe newborn diarrhea is still not well known. We aimed to determine the seasonal and age-associated pathogen distribution of severe diarrhea in newborn calves admitted to the intensive care unit (ICU) of Erciyes University animal hospital over a year. Fecal samples were collected during the ICU admissions, and specimens were subjected to a diarrheal pathogen screening panel that included bovine coronavirus (BCoV), Cryptosporidium spp., ETEC K99+, and bovine rotavirus, using RT-PCR and conventional PCR methods. Further isolation experiments were performed with permissive cell cultures and bacterial enrichment methods to identify the clinical importance of infectious pathogen shedding in the ICU. Among the hospitalized calves aged less than 45 days old, the majority of calves originated from small farms (85.9%). The pathogen that most frequently occurred was Cryptosporidium spp. (61.5%) followed by rotavirus (56.4%). The frequency of animal admission to ICU and GI pathogen identification was higher during the winter season (44.9%) when compared to other seasons. Most calves included in the study were 1-6 days old (44.9%). Lastly, co-infection with rotavirus and Cryptosporidium spp. occurred more frequently than other dual or multi-infection events. This study was the first to define severe diarrhea-causing GI pathogens from ICU admitted newborn calves in Turkey.

Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Simple Summary

Recently, there has been increasing attention focused on the intestinal microflorae of animals due to their critical role in maintaining health and preventing disease. With the improvement of the Chinese national economy and the people’s material standard of living, the beef cattle industry is growing rapidly to meet the growing market demand for beef. Mongolian cattle is a precious genetic resource in China and an excellent cattle breed in Inner Mongolia. However, updated research on topics concerning the gut microbiota of Mongolian cattle are absent. Therefore, this study focused on the differences in the gut microbiota composition of Mongolian cattle in different geographical environments. The gut microbiota composition of the Mongolian cattle from the grasslands was relatively similar, while that from the desert areas was different. The results of this study contribute to our understanding of the influence of geographical factors on the composition of gut microbiota in Mongolian cattle.

Abstract

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

Use of Lactobacillus plantarum (strains 22F and 25F) and Pediococcus acidilactici (strain 72N) as replacements for antibiotic-growth promotants in pigs

The lactic acid bacteria (LAB) Lactobacillus plantarum (strains 22F and 25F) and Pediococcus acidilactici (strain 72N) have appeared promising as replacements for antibiotics in in vitro studies. Microencapsulation, especially by the spray-drying method, has been used to preserve their numbers and characteristics during storage and digestion. This study compared the efficacy of these strains and their microencapsulated form with antibiotic usage on growth performance, faecal microbial counts, and intestinal morphology in nursing-finishing pigs. A total of 240 healthy neonatal pigs were treated on days 0, 3, 6, 9, and 12 after cross-fostering. Sterile peptone water was delivered orally to the control and antibiotic groups. Spray-dried Lactobacillus plantarum strain 22F stored for 6-months was administered to piglets in the spraydry group. Three ml of each the three fresh strains (10⁹ CFU/mL) were orally administered to piglets in each group. All pigs received the basal diets, but these were supplemented with routine antibiotic for the antibiotic group. Pigs in all the probiotic supplemented groups exhibited a better average daily gain and feed conversion ratio than those of the controls in the nursery and grower phases. Probiotic supplementation increased viable lactobacilli and decreased enterobacterial counts. Antibiotic additives reduced both enterobacterial and lactobacilli counts. Villous height and villous height:crypt depth ratio were greater in probiotic and antibiotic supplemented pigs comparing to the controls, especially in the jejunum. The results demonstrated the feasibility of using these strains as a substitute for antibiotics and the practicality of the microencapsulation protocol for use in swine farms.

Effects of Antibiotic Treatment and Probiotics on the Gut Microbiome of 40 Infants Delivered Before Term by Cesarean Section Analysed by Using 16S rRNA Quantitative Polymerase Chain Reaction Sequencing

BACKGROUND This study aimed to investigate the effects on the gut microbiome of 40 infants delivered before term by cesarean section between antibiotic treatment and probiotics as assessed by 16S rRNA quantitative polymerase chain reaction (qPCR) sequencing. MATERIAL AND METHODS We divided 40 premature infants delivered by cesarean section into 4 groups according to exposure to antibiotics or probiotics: N group (No-probiotics and No-antibiotics), A group (antibiotics), P group (probiotics), and the AP group (antibiotics+probiotics). Fecal samples were collected on days 1, 3, and 10, and the microflora data were generated using 16S rRNA qPCR sequencing technology. The BugBase tool was used for phenotype prediction, the Tax4Fun tool was used for function prediction, and iPath software was used to predict the metabolic pathways of intestinal bacteria. RESULTS Antibiotics increased the abundance of pathogenic bacteria and reduced the replication and repair function (P=0.049), nucleotide metabolism function (P=0.047), and the purine metabolism pathways (P<0.05) of the gut microbiota. Probiotics increased the abundance of beneficial bacteria and the cellular community prokaryote function (P=0.042) and contributed to the Bifidobacteria biofilm formation. Probiotics alleviated the damage of antibiotics to the composition and function of the gut microbiota. CONCLUSIONS The findings from this study showed that antibiotic treatment of preterm infants born by cesarean section changed the gut microbiome, but that the use of probiotics could restore the normal microbiome, which supports that restoration of the normal gut microbiota may be achieved with probiotics.

Effects of Rearing Conditions and Sex on Cecal Microbiota in Ducks

The intestinal microbiome influences the health of animals. However, little is known about the impact of indoor conditions and sex on intestinal microbiome diversity and composition in ducks. The present study aimed to investigate differences in the cecal microbiome between male and female ducks reared on the floor (PY group) or in cages (LY group). We also determined the relationships between cecal microbiota composition and slaughter traits, and the expression levels of mucosal and intestinal structural genes in ducks. There was a slight difference in slaughter traits among the groups, with cecum weight being significantly lighter in the LY compared with the PY group, especially in females (p < 0.05). Analysis of the alpha diversity of the cecal microbiota between males and females in the LY and PY groups showed that LY males had significantly lower diversity and richness. Beta diversity analysis demonstrated differences in the microbiota composition in relation to rearing conditions, and a significant difference between the sexes in the PY groups. The dominant bacterial phyla in duck cecum were Bacteroidetes, Firmicutes, Proteobacteria, and Fusobacteria. The relative abundances of the most common bacteria revealed that the intestinal microbiota diversity and composition were affected by both feeding conditions and sex. Several bacterial genera were detected differentially among the groups. These genera were correlated with slaughter traits and expression levels of mucosal and cecal structural genes in ducks. In conclusion, rearing conditions, sex, and associated changes in the cecal microbiota are thus associated with gut barrier functions in ducks.

Engineering the cbh1 Promoter of Trichoderma reesei for Enhanced Protein Production by Replacing the Binding Sites of a Transcription Repressor ACE1 to Those of the Activators

The strong and inducible cbh1 promoter is most widely used to express heterologous proteins, useful in food and feed industries, in Trichoderma reesei. Enhancing its ability to direct transcription provides a general strategy to improve protein production in T. reesei. The cbh1 promoter was engineered by replacing eight binding sites of the transcription repressor ACE1 to those of the activators ACE2, Hap2/3/5, and Xyr1. While changing ACE1 to Hap2/3/5-binding sites completely abolished the transcription ability, replacements with ACE2- and Xyr1-binding sites (designated cbh1pA and cbh1pX promoters, respectively) largely improved the promoter transcription efficiency, as reflected by expression of a reporter gene DsRed. The cbh1pA and cbh1pX promoters were applied to improve secretory expression of a codon-optimized mannanase from Aspergillus niger to 3.6- and 5.0-fold higher, respectively, which has high application potential in feed industry.

Analysis of microbial diversity and composition in small intestine during different development times in ducks

We studied the microbial profiles of the duodenum, jejunum, and ileum during different developmental stages in the duck using high-throughput sequencing of the bacterial 16S rRNA gene. We also investigated the differences in the microbiota in the duodenum, jejunum, and ileum at different developmental times. A correlation analysis was performed between the most abundant bacterial genera and the development of the small intestine. An analysis of alpha diversity indicated different species richness and bacterial diversity in the different small intestinal segments and at different development times. A beta diversity analysis indicated differences in the bacterial community compositions across time. In a weighted UniFrac principal coordinates analysis, the samples clustered into two categories, 2 to 4 wk and 6 to 10 wk, in the duodenum, jejunum, and ileum. Our results show that the small intestine is predominantly populated by the phyla Firmicutes, Bacteroidetes, and Proteobacteria throughout the developmental stages of the duck. The duodenum, jejunum, and ileum shared most of the bacterial phyla and genera present, although they showed significant differences in their relative abundances in the intestinal segments and developmental stages. They shared different bacterial taxa during development times and among different segments when the intergroup differences were analyzed. The genera Bacillus, Corynebacterium 1, Lactococcus, Sphingomonas, and Haliangium correlated moderately positively with the increase in bodyweight and the lengths and weights of the duodenum, jejunum, and ileum, and these genera may be considered important markers when assessing the heath of the intestinal microbiota in ducks. This study provides a foundation upon which to extend our knowledge of the diversity and composition of the duck microbiota and a basis for further studies of the management of the small intestinal microbiota and improvements in the health and production of ducks.

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

Comparing the effect of intestinal bacteria from rabbit, pig, and chicken on inflammatory response in cultured rabbit crypt and villus

Rabbit is susceptible to intestinal infection, which often results in severe inflammatory response. To investigate whether the special community structure of rabbit intestinal bacteria contributes to this susceptibility, we compared the inflammatory responses of isolated rabbit crypt and villus to heat-treated total bacteria in pig, chicken, and rabbit ileal contents. The dominant phylum in pig and chicken ileum was Firmicutes, while Bacteroidetes was dominant in rabbit ileum. The intestinal bacteria from rabbit induced higher expression of toll-like receptor 4 (TLR4) in rabbit crypt and villus (P < 0.05). TLR2 and TLR3 expression was obviously stimulated by chicken and pig intestinal bacteria (P < 0.05) but not by those of rabbit. The ileal bacteria from those three animals all increased the expression of tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6) in crypts and villus (P < 0.05). Chicken and pig ileal bacteria also stimulated the expression of anti-inflammatory factors interferon beta (IFN-β) and IL-10 (P < 0.05), while those of rabbit did not (P > 0.05). In conclusion, a higher abundance of Gram-negative bacteria in rabbit ileum did not lead to more expressive pro-inflammatory cytokines in isolated rabbit crypt and villus, but a higher percentage of Lactobacillus in chicken ileum might result in more expressive anti-inflammatory factors.

The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals

The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.

Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children

BACKGROUND

Alterations in the intestinal microbiota have been associated with the development of allergic diseases, such as asthma and food allergies. However, there is no report detailing the role of microbiota alterations in Henoch-Schönlein Purpura (HSP) development.

METHOD

A total of 85 children with HSP and 70 healthy children were recruited for this study. Intestinal microbiota composition was analyzed by 16S rRNA gene-based pyrosequencing. Fecal microbial diversity and composition were compared.

RESULT

We compared the gut microbiota of 155 subjects and found that children with HSP exhibited gut microbial dysbiosis. Lower microbial diversity and richness were found in HSP patients when compared to the control group. Based on an analysis of similarities, the composition of the microbiota in HSP patients was also different from that of the control group (r = 0.306, P = 0.001). The relative abundance of the bacterial genera Dialister (P < 0.0001), Roseburia (P < 0.0001), and Parasutterella (P < 0.0001) was significantly decreased in HSP children, while the relative abundance of Parabacteroides (P < 0.006) and Enterococcus (P < 0.0001) in these children was significantly increased. Based on Spearman correlation analysis, the LOS showed a significant negative (P < 0.05) correlation with the genera Paraprevotella and Roseburia. Meanwhile, IgA levels exhibited a significant negative (P < 0.01) correlation with the genus Bifidobacterium.

CONCLUSIONS

Our results indicate that HSP is associated with significant compositional and structural changes in the gut microbiota. These results enhance the potential for future microbial-based therapies to improve the clinical outcome of HSP in children.

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil^® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin^® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age

BACKGROUND

Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts.

RESULTS

Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species. Furthermore, in silico analyses allowed the reconstruction of the genome sequences of five ancient bacterial genomes, including apparent pathogenic ancestor strains of Clostridium perfringens and Pseudomonas veronii species present in the gut of the Tyrolean Iceman.

CONCLUSIONS

Genomic analyses of the reconstructed C. perfringens chromosome clearly support the occurrence of a pathogenic profile consisting of virulence genes already existing in the ancient strain, thereby reinforcing the notion of a very early speciation of this taxon towards a pathogenic phenotype. In contrast, the evolutionary development of P. veronii appears to be characterized by the acquisition of antibiotic resistance genes in more recent times as well as an evolution towards an ecological niche outside of the (human) gastrointestinal tract.

The 5300-year-old Helicobacter pylori genome of the Iceman

The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The "Iceman" H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community

Recovery of high quality PCR-amplifiable DNA has been the general minimal requirement for DNA extraction methods for bulk molecular analysis. However, modern high through-put community profiling technologies are more sensitive to representativeness and reproducibility of DNA extraction method. Here, we assess the impact of three DNA extraction methods (with different levels of extraction harshness) for assessing hindgut microbiomes from pigs fed with different diets (with different physical properties). DNA extraction from each sample was performed in three technical replicates for each extraction method and sequenced by 16S rRNA amplicon sequencing. Host was the primary driver of molecular sequencing outcomes, particularly on samples analysed by wheat based diets, but higher variability, with one failed extraction occurred on samples from a barley fed pig. Based on these results, an effective method will enable reproducible and quality outcomes on a range of samples, whereas an ineffective method will fail to generate extract, but host (rather than extraction method) remains the primary factor.

Effects of Fuzhuan Brick-Tea Water Extract on Mice Infected with E. coli O157:H7

Fuzhuan brick-tea extract (FBTE) affects the physiology of mice infected with Escherichia coli O157:H7. For 10 consecutive days, 0.05, 0.5, and 1.0 g/mL FBTE was administered intragastrically to three groups of infected Kunming mice, and changes in immunological function, hematology, and histopathology were examined. The results revealed upregulation of platelets, total protein, and albumin along with downregulation of serum triglycerides, aspartate aminotransferase, creatinine, and urea nitrogen in FBTE-treated mice. Histological sections of stomach, kidney, duodenum, ileum, and colon suggested that infected mucous membranes could be rehabilitated by low- and high-dose FBTE and that inflammation was alleviated. Similarly, increased thymic function in mice treated with middle- and high-dose FBTE led to elevated serum hemolysin antibody titer and increased CD4⁺ and CD8⁺ T cells, as indicated by CD4⁺ and CD8⁺ expression on intestinal mucosa. Monocyte and macrophage function was improved by three FBTE dosages tested. Colonic microbiota analysis by denaturing gradient gel electrophoresis (DGGE) revealed characteristic bands in infected mice treated with middle- and high-dose FBTE and increased species diversity in Lactobacillus, Bacteroides, and Clostridium cluster IV. These results suggest that FBTE may protect kidney and liver of mice infected with E. coli O157:H7, improve immune function, and regulate the colonic microbiota.

Noninvasive method of DNA isolation from fecal epithelial tissue of dairy animals

A novel noninvasive genomic DNA isolation protocol from fecal tissue, by the proteinase K digestion and guanidine hydrochloride extraction method, was assessed for the genotyping of cattle and buffalo. The epithelial tissues present on the surface of the feces were used as source for isolation of genomic DNA. The DNA isolated from fecal tissue was found to be similar as those obtained from other body tissues such as skin, brain, liver, kidney, and muscle. The quality of DNA was checked by agarose gel electrophoresis and polymerase chain reaction (PCR). We successfully amplified a 320 bp MHC class II DRB gene and a 125 bp mt-DNA D-loop region from isolated genomic DNA of cattle. Thus, the DNA isolated using this method was suitable for common molecular biology methods, such as restriction enzyme digestion and genotyping of dairy animals through PCR.

A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the "gold standard" enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples.

Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples

Next-generation sequencing (NGS) technology has extraordinarily enhanced the scope of research in the life sciences. To broaden the application of NGS to systems that were previously difficult to study, we present protocols for processing faecal and swab samples into amplicon libraries amenable to Illumina sequencing. We developed and tested a novel metagenomic DNA extraction approach using solid phase reversible immobilization (SPRI) beads on Western Bluebird (Sialia mexicana) samples stored in RNAlater. Compared with the MO BIO PowerSoil Kit, the current standard for the Human and Earth Microbiome Projects, the SPRI-based method produced comparable 16S rRNA gene PCR amplification from faecal extractions but significantly greater DNA quality, quantity and PCR success for both cloacal and oral swab samples. We furthermore modified published protocols for preparing highly multiplexed Illumina libraries with minimal sample loss and without post-adapter ligation amplification. Our library preparation protocol was successfully validated on three sets of heterogeneous amplicons (16S rRNA gene amplicons from SPRI and PowerSoil extractions as well as control arthropod COI gene amplicons) that were sequenced across three independent, 250-bp, paired-end runs on Illumina's MiSeq platform. Sequence analyses revealed largely equivalent results from the SPRI and PowerSoil extractions. Our comprehensive strategies focus on maximizing efficiency and minimizing costs. In addition to increasing the feasibility of using minimally invasive sampling and NGS capabilities in avian research, our methods are notably not avian-specific and thus applicable to many research programmes that involve DNA extraction and amplicon sequencing.

Comparison of seven methods for extraction of bacterial DNA from fecal and cecal samples of mice

Analysis of bacterial DNA from fecal samples of mice is commonly performed in experimental studies. Although DNA extraction is a critical step in various molecular approaches, the efficiency of methods that may be used for DNA extraction from mice fecal samples has never been evaluated. We compared the efficiencies of six widely used commercial kits (MasterPure™ Gram Positive DNA Purification Kit, QIAamp® DNA Stool Mini Kit; NucliSENS® easyMAG®, ZR Fecal DNA MiniPrep™, FastDNA® SPIN Kit for Feces and FastDNA® SPIN Kit for Soil) and a non-commercial method for DNA isolation from mice feces and cecal contents. DNA quantity and quality were assessed by fluorometry, spectrophotometry, gel electrophoresis and qPCR. Cell lysis efficiencies were evaluated by qPCR targeting three relevant bacteria in spiked specimens. For both feces and intestinal contents, the most efficient extraction method was the FastDNA® SPIN Kit for Soil.

Metagenomic analysis reveals presence of Treponema denticola in a tissue biopsy of the Iceman

Ancient hominoid genome studies can be regarded by definition as metagenomic analyses since they represent a mixture of both hominoid and microbial sequences in an environment. Here, we report the molecular detection of the oral spirochete Treponema denticola in ancient human tissue biopsies of the Iceman, a 5,300-year-old Copper Age natural ice mummy. Initially, the metagenomic data of the Iceman’s genomic survey was screened for bacterial ribosomal RNA (rRNA) specific reads. Through ranking the reads by abundance a relatively high number of rRNA reads most similar to T. denticola was detected. Mapping of the metagenome sequences against the T. denticola genome revealed additional reads most similar to this opportunistic pathogen. The DNA damage pattern of specifically mapped reads suggests an ancient origin of these sequences. The haematogenous spread of bacteria of the oral microbiome often reported in the recent literature could already explain the presence of metagenomic reads specific for T. denticola in the Iceman’s bone biopsy. We extended, however, our survey to an Iceman gingival tissue sample and a mouth swab sample and could thereby detect T. denticola and Porphyrimonas gingivalis, another important member of the human commensal oral microflora. Taken together, this study clearly underlines the opportunity to detect disease-associated microorganisms when applying metagenomics- enabled approaches on datasets of ancient human remains.

Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real-time PCR

Four commercial DNA extraction kits and a minor modification in the DNA elution procedure were evaluated for the quantitation of bacteria in pig manure samples. The PowerSoil®, PowerFecal®, NucleoSpin® Soil kits and QIAamp® DNA Stool Mini kit were tested on raw manure samples and on lagoon effluents for their ability to quantify total bacteria and a subdominant bacteria specific of pig manure contamination: Lactobacillus amylovorus. The NucleoSpin® Soil kit (NS kit), and to a lesser extent the PowerFecal® kit were the most efficient methods. Regardless of the kit utilized, the modified elution procedure increased DNA yield in the lagoon effluent by a factor of 1.4 to 1.8. When tested on 10 piggery effluent samples, compared to the QIAamp kit, the NS kit combined with the modified elution step, increased by a factor up to 1.7 log₁₀ the values of the concentration of L. amylovorus. Regardless of the type of manure, the best DNA quality and the highest concentrations of bacteria were obtained using the NS kit combined with the modification of the elution procedure. The method recommended here significantly improved quantitation of subdominant bacteria in manure.

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal samples using three different extraction methods. No consistent differences were observed in DNA yields between extractions on fresh and frozen samples; however, differences were observed between extraction methods. Quantitative PCR analysis was subsequently performed on all DNA samples using six different primer pairs targeting 16S rRNA genes of significant bacterial groups, and the community composition was evaluated by comparing specific ratios of the calculated abundances. In seven of nine cases, the Firmicutes to Bacteroidetes 16S rRNA gene ratio was significantly higher in fecal samples that had been frozen compared to identical samples that had not. This effect was further supported by qPCR analysis of bacterial groups within these two phyla. The results demonstrate that storage conditions of fecal samples may adversely affect the determined Firmicutes to Bacteroidetes ratio, which is a frequently used biomarker in gut microbiology.