Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum and ileum in broiler chickens.

Coccidiosis, an intestinal disease caused by Eimeria parasites, is responsible for major losses in the poultry industry by impacting chicken health. The gut microbiota is associated with health factors, such as nutrient exchange and immune system modulation, requiring understanding on the effects of Eimeria infection on the gut microbiota. This study aimed to determine the effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the cecum (CeL and CeM) and ileum (IlL and IlM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. E. acervulina infection decreased evenness in CeL microbiota at day 10, increased richness in CeM microbiota at day 3 before decreasing richness at day 14, and decreased richness in IlL microbiota from day 3 to 10. CeL, CeM, and IlL microbiota differed between infected and control birds based on beta diversity at varying time points. Infection reduced relative abundance of bacterial taxa and some predicted metabolic pathways known for short-chain fatty acid production in CeL, CeM, and IlL microbiota, but further understanding of metabolic function is required. Despite E. acervulina primarily targeting the duodenum, our findings demonstrate the infection can impact bacterial diversity and abundance in the cecal and ileal microbiota.

Low-level pathogen infection and geographic location correlate with the skin microbiomes of Columbia spotted frogs (Rana luteiventris) in a montane landscape.

The skin microbiome of amphibians can influence host susceptibility towards the fungal pathogen Batrachochytrium dendrobatidis (Bd), while simultaneously having the potential to be altered by Bd. Severe Bd infections are known to alter the amphibian skin microbiome; however, little is known about microbiome interactions in amphibians with low infection intensity. In addition to disease dynamics, environmental factors may influence the microbiome. To test for patterns in bacterial diversity based on pathogen infection and environmental factors, 399 Columbia spotted frogs (Rana luteiventris) were sampled throughout northern Idaho and northeastern Washington across two years. Bd prevalence and intensity were measured in 376 frogs, revealing a prevalence of 69%, but generally low infection intensity (Mean = 127 Bd zoospore equivalents among infected frogs). Skin bacterial communities were characterized in 92 frogs using 16S rRNA gene amplicon sequencing. Our results indicated correlations of decreasing Shannon diversity and evenness as infection intensity increased. Latitude was correlated with bacterial richness and Faith's Phylogenetic Diversity measures, indicating increased diversity in northern locations. Beta diversity (UniFrac) analyses revealed that skin microbiomes were distinct between infected and uninfected frogs, and infection intensity had a significant effect on microbiome composition. Site explained the majority of microbiome variation (weighted UniFrac: 57.5%), suggesting a combination of local habitat conditions explain variation, as only small proportions of variation could be explained by year, month, temperature, elevation, and latitude individually. Bacterial genera with potential for Bd-inhibitory properties were found with differential relative abundance in infected and uninfected frogs, with higher Stenotrophomonas and lower Pseudomonas relative abundance observed in infected frogs. Further study may indicate if Bd inhibition by members of the skin microbiome is an influence behind the low infection intensities observed and whether low Bd infection intensities are capable of altering skin microbiome composition.

Cecal microbiota composition differs under normal and high ambient temperatures in genetically distinct chicken lines.

Modern broilers, selected for high growth rate, are more susceptible to heat stress (HS) as compared to their ancestral jungle fowl (JF). HS affects epithelia barrier integrity, which is associated with gut microbiota. The aim of this study was to determine the effect of HS on the cecal luminal (CeL) and cecal mucosal (CeM) microbiota in JF and three broiler populations: Athens Canadian Random Bred (ACRB), 1995 Random Bred (L1995), and Modern Random Bred (L2015). Broiler chicks were subjected to thermoneutral TN (24 °C) or chronic cyclic HS (8 h/day, 36 °C) condition from day 29 until day 56. HS affected richness in CeL microbiota in a line-dependent manner, decreasing richness in slow-growing JF and ACRB lines, while increasing richness in faster-growing L1995 and L2015. Microbiota were distinct between HS and TN conditions in CeL microbiota of all four lines and in CeM microbiota of L2015. Certain bacterial genera were also affected in a line-dependent manner, with HS tending to increase relative abundance in CeL microbiota of slow-growing lines, while decreases were common in fast-growing lines. Predictive functional analysis suggested a greater impact of HS on metabolic pathways in L2015 compared to other lines.

Effects of codon optimization on expression in Escherichia coli of protein-coding DNA sequences from the protozoan Eimeria.

The objective of this study was to compare the levels of recombinant protein from three Eimeria genes before and after optimization of codons for expression in Escherichia coli. Protein coding sequences from Eimeria maxima (EmaxSO7, EmaxIMP1) and Eimeria acervulina (EAH00033530) were cloned with or without prior codon optimization and expressed as polyHis fusion proteins. All three outcomes: higher, lower, or no change in the yield of amount of recombinant protein were observed suggesting that codon optimization alone for expression in E. coli does not inevitably lead to higher expression levels. Analysis of codon usage for each gene sequence revealed that, similar to other organisms, Eimeria intersperses rare and frequently used codons in protein-coding sequences. However, no relationship was observed between the predicted protein structure and the location of major and minor codons, suggesting that codon selection in this apicomplexan parasite is influenced by factors other than regional secondary protein structure.

Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens.

The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.

Genome Resources for the Colletotrichum gloeosporioides Species Complex: 13 Tree Endophytes from the Neotropics and Paleotropics.

Thirteen draft genome assemblies are presented for four Colletotrichum gloeosporioides complex species, namely, Colletotrichum aeschynomenes, Colletotrichum asianum, Colletotrichum fructicola, and Colletotrichum siamense, which were isolated from tropical tree hosts as endophytes.

Draft Genome Sequence of the Sophorolipid-Producing Yeast Pseudohyphozyma bogoriensis ATCC 18809.

Pseudohyphozyma bogoriensis is gaining attention as a microbial source of high-value sophorolipids. We report here on its genomic sequence, which will improve our understanding of its metabolic pathways and allow the development of genome manipulation systems. PacBio sequencing was performed, yielding a 26-Mbp genome with 57% GC content and encoding 7,847 predicted proteins.

Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens.

BACKGROUND: The first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization. In the current broiler production system, chicks may not receive feed and water for 24 to 72 h due to variations in hatching time and hatchery management. Post-hatch feed delay affects body weight, feed efficiency, mortality, and gut development. The goal of this study was to investigate changes in the microbiome in broiler chickens early PH and the effect of delayed access to feed on the microbiota. RESULTS: Chicks either received feed and water immediately after hatch or access to feed was delayed for 48 h to mimic commercial hatchery settings (treatment, TRT). Both groups were sampled (n = 6) at -48, 0, 4 h, and 1 (24 h), 2 (48 h), 3 (72 h), 4 (96 h), 6 (144 h), 8 (192 h), 10 (240 h), 12 (288 h) and 14 (336 h) days PH. Ileal (IL) and cecal (CE) epithelial scrapings (mucosal bacteria, M) and digesta (luminal bacteria, L) were collected for microbiota analysis. Microbiota was determined by sequencing the V3-V4 region of bacterial 16S rRNA and analyzed using QIIME2. The microbiota of early ileal and cecal samples were characterized by high abundance of unclassified bacteria. Among four bacterial populations (IL-L, IL-M, CE-L, CE-M), IL-M was the least affected by delayed access to feed early PH. Both alpha and beta diversities were affected by delayed access to feed PH in IL-L, CE-M and CE-L. However, the development effect was more pronounced. In all four bacterial populations, significant changes due to developmental effect (time relative to hatch) was observed in taxonomic composition, with transient changes of bacterial taxa during the first two weeks PH. Delayed access to feed has limited influence on bacterial composition with only a few genera and species affected in all four bacterial populations. Predicted function based on 16S rRNA was also affected by delayed access to feed PH with most changes in metabolic pathway richness observed in IL-L, CE-L and CE-M. CONCLUSIONS: These results show transient changes in chicken microbiota biodiversity during the first two weeks PH and indicate that delayed access to feed affects microbiota development. Proper microbiota development could be an important factor in disease prevention and antibiotic use in broiler chickens. Moreover, significant differences in response to delayed access to feed PH between luminal and mucosal bacterial populations strongly suggests the need for separate analysis of these two populations.

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota.

The chicken microbiota is often analyzed to address questions about the effects of diet or disease on poultry health. To analyze the microbiota, bioinformatic platforms such as QIIME 2 and mothur are used, which incorporate public taxonomic databases such as Greengenes, the ribosomal database project (RDP), and SILVA to assign taxonomies to bacterial sequences. Many chicken microbiota studies continue to incorporate the Greengenes database, which has not been updated since 2013. To determine whether a choice of database could affect results, this study compared the results of bioinformatic analyses obtained using the Greengenes, RDP, and SILVA databases on a cecal luminal microbiome dataset. The QIIME 2 platform was used to process 16S bacterial sequences and assign taxonomies with Greengenes, RDP, and SILVA. Linear discriminant analysis effect size (LEfSe) was performed, allowing for the comparison of taxonomies considered significantly differentially abundant between the three databases. Some notable differences between databases were observed in results, in particular the ability of SILVA database to classify members of the family Lachnospiraceae into separate genera, while these members remained in one group of unclassified Lachnospiraceae through Greengenes and RDP. LEfSe analyses showed that the SILVA database produced more differentially abundant genera, in large part due to the classification of these separate Lachnospiraceae genera. Additionally, the relative abundance of unclassified Lachnospiraceae in SILVA results was significantly lower than in RDP results. Our results show the choice of taxonomic database can influence the results of a microbiota study at the genus level, potentially affecting the interpretation of the results. The use of the SILVA database is recommended over Greengenes in chicken microbiota studies, as more specific classifications at the genus level may provide more accurate interpretations of changes in the microbiota.

Effects of Eimeria tenella on Cecal Luminal and Mucosal Microbiota in Broiler Chickens.

The intestinal disease coccidiosis, caused by parasitic Eimeria species, severely impacts poultry production, leading to an estimated $14 billion in annual losses worldwide. As the poultry industry moves away from antibiotics as a treatment for diseases, a better understanding of the microbiota is required to develop other solutions such as probiotics, prebiotics, and nutritional supplements. This study aimed to investigate the effects of Eimeria tenella infection on luminal (cecal contents [CeC]) and mucosal (cecal epithelial scrapings [CeS]) microbial populations in 288 Ross 708 broiler chickens at multiple time points postinfection (PI). By use of 16S rRNA amplicon sequencing, it was revealed that microbial diversity differed in infected (IF) chickens in comparison to the control (C) in both CeC and CeS microbiota at the peak of infection (7 days PI), when simultaneously IF birds saw reduced body weight gain and a higher feed conversion ratio. Infection resulted in a significant differential abundance of some bacterial taxa, including increases in potential secondary pathogens Escherichia coli, Enterococcus, Clostridium, and Proteus and a decrease in the short chain fatty acid-producing family Lachnospiraceae. Predicted metagenomic pathways associated with E. coli, such as those responsible for amino acid biosynthesis, were differentially expressed in IF birds. In conclusion, our results show that E. tenella infection disturbs luminal and mucosal microbiota balance in chickens. Moreover, the luminal microbiota seems to be more susceptible to prolonged imbalance due to IF, whereas the mucosal microbiota appeared to be affected only in the short term, demonstrating the importance of researching both the luminal and mucosal microbiota of the cecum.

Efectos de Eimeria tenella sobre la microbiota luminal y de la mucosa de los ciegos en pollos de engorde. La coccidiosis, una enfermedad intestinal causada por especies parasitarias de Eimeria, afecta gravemente la producción avícola, lo que genera pérdidas anuales estimadas en 14,000 millones de dólares en todo el mundo. A medida que la industria avícola se aleja de los antibióticos como tratamiento para enfermedades, se requiere de un mejor conocimiento de la microbiota para desarrollar otras soluciones como probióticos, prebióticos y suplementos nutricionales. Este estudio tuvo como objetivo investigar los efectos de la infección por Eimeria tenella en las poblaciones microbianas luminales (contenido cecal [CeC]) y de la mucosa (raspados del epitelio cecal [CeS]) en pollos de engorde Ross 708 (288) en diferentes puntos de tiempo después de la infección (PI). Mediante el uso de la secuenciación de amplicones de ARNr 16S, se reveló que la diversidad microbiana difería en los pollos infectados (IF) en comparación con el grupo control (C) tanto en la microbiota del contenido cecal como de la mucosa durante el pico de infección (7 días después de la infección), cuando de manera simultánea las aves infectadas mostraron una reducción en la ganancia de peso corporal reducido y una tasa de conversión alimenticia más alta. La infección resultó en una abundancia diferencial significativa de algunos taxones bacterianos, incluidos aumentos en los patógenos secundarios potenciales como Escherichia coli, Enterococcus, Clostridium y Proteus y una disminución en la familia Lachnospiraceae productora de ácidos grasos de cadena corta. Las vías metagenómicas predichas asociadas con E. coli, como las responsables de la biosíntesis de aminoácidos, se expresaron diferencialmente en las aves infectadas. En conclusión, estos resultados muestran que la infección por E. tenella perturba el equilibrio de la microbiota luminal y de la mucosa en pollos. Además, la microbiota luminal parece ser más susceptible a un desequilibrio prolongado debido a la infección, mientras que la microbiota mucosa parece verse afectada solo a corto plazo, lo que demuestra la importancia de investigar tanto la microbiota luminal como la de la mucosa en el ciego.