Image_2_Rumen and fecal microbiota profiles associated with immunity of young and adult goats.tif

Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.</p

Image_2_Plants Grown in Parafilm-Wrapped Petri Dishes Are Stressed and Possess Altered Gene Expression Profile.tif

Arabidopsis is used as a model species in numerous physiological and genetic studies. Most of them employ parafilm-wrapped sterile culture. Here we demonstrate that this method is prone to potential artifacts and can lead to erroneous conclusions. We compared the effect of different sealing methods including air-permeable paper tape and traditional parafilm on Arabidopsis seedling growth, root development and gene expression network. Although seedlings grown in Petri dishes after 1 week sealed with paper tape showed a similar growth phenotype to that of parafilm-sealed seedlings, more than 700 differentially expressed genes (DEG) were found, including stress and nutrition-responsive genes. In addition, more H2O2 was accumulated in the tissues of parafilm-sealed plants. After 14 days of growth, paper tape-sealed plants grew much better than parafilm-sealed ones and accumulated higher chlorophyll content, with 490 DEGs found. After 3 weeks of growth, paper tape-sealed plants had higher chlorophyll and better growth compared to parafilm-sealed ones; and only 10 DEGs were found at this stage. Thus, the obvious phenotype observed at the latter stage was a result of differential gene expression at earlier time points, mostly of defense, abiotic stress, nutrition, and phytohormone-responsive genes. More O2 content was detected inside paper tape-sealed Petri dishes at early growth stage (7 days), and distinct difference in the CO2 content was observed between parafilm-sealed and paper tape-sealed Petri dishes. Furthermore, the carbon source also influenced seedlings growth with different sealing methods. In conclusion, conventional sealing using parafilm was not the optimal choice, most likely because of the limited gas exchange and a consequent stress caused to plants.</p

DataSheet2_Multi-Year Survey and Bayesian Modeling Approach for Characterizing Arsenic Pollution in Marine Clams Cultivated Along the Tidal Flats of Mid-Eastern China.DOCX

Marine clam is one of the main sources of arsenic (As), and the tidal flats of Jiangsu Province are considered major culturing areas for clams in mid-eastern China. In view of increasingly severe pollution in this region, concerns have been raised by the consumers with the safety of clams they purchased or may purchase. To address these concerns, we conducted a multi-year survey to determine the levels of As and As species in five major clam species cultivated in eight production areas of this region. Based on the above analysis data, Bayesian statistics used a Markov Chain Monte Carlo approach was applied to predict the toxic As residue distributions in clams produced in this region and their health risks to Chinese adults. It was found that the bioaccumulation ability of total As (tAs) and inorganic As (iAs) was species-specific, while Mactra veneriformis (MV) had the strongest accumulation capacity for toxic iAs (0.22–2.85 mg/kg dw). Up to 6.7% of the tested MV samples exceeding the iAs limit of China Food and Drug Administration. The content of iAs was also found to be related significantly to the harvest seasons, with clam in the spawning period (June) having the lowest iAs concentrations. The non-carcinogenic and carcinogenic health risk from dietary exposure to iAs associated with MV consumption was rather high, which suggested that specific attention should be paid to the safety of clam consumption in this region.</p

Image_1_Rumen and fecal microbiota profiles associated with immunity of young and adult goats.tif

Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.</p

Table_1_Plants Grown in Parafilm-Wrapped Petri Dishes Are Stressed and Possess Altered Gene Expression Profile.DOCX

Arabidopsis is used as a model species in numerous physiological and genetic studies. Most of them employ parafilm-wrapped sterile culture. Here we demonstrate that this method is prone to potential artifacts and can lead to erroneous conclusions. We compared the effect of different sealing methods including air-permeable paper tape and traditional parafilm on Arabidopsis seedling growth, root development and gene expression network. Although seedlings grown in Petri dishes after 1 week sealed with paper tape showed a similar growth phenotype to that of parafilm-sealed seedlings, more than 700 differentially expressed genes (DEG) were found, including stress and nutrition-responsive genes. In addition, more H2O2 was accumulated in the tissues of parafilm-sealed plants. After 14 days of growth, paper tape-sealed plants grew much better than parafilm-sealed ones and accumulated higher chlorophyll content, with 490 DEGs found. After 3 weeks of growth, paper tape-sealed plants had higher chlorophyll and better growth compared to parafilm-sealed ones; and only 10 DEGs were found at this stage. Thus, the obvious phenotype observed at the latter stage was a result of differential gene expression at earlier time points, mostly of defense, abiotic stress, nutrition, and phytohormone-responsive genes. More O2 content was detected inside paper tape-sealed Petri dishes at early growth stage (7 days), and distinct difference in the CO2 content was observed between parafilm-sealed and paper tape-sealed Petri dishes. Furthermore, the carbon source also influenced seedlings growth with different sealing methods. In conclusion, conventional sealing using parafilm was not the optimal choice, most likely because of the limited gas exchange and a consequent stress caused to plants.</p

Table_2_Rumen and fecal microbiota profiles associated with immunity of young and adult goats.docx

Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.</p

Table1_Multi-Year Survey and Bayesian Modeling Approach for Characterizing Arsenic Pollution in Marine Clams Cultivated Along the Tidal Flats of Mid-Eastern China.XLS

Marine clam is one of the main sources of arsenic (As), and the tidal flats of Jiangsu Province are considered major culturing areas for clams in mid-eastern China. In view of increasingly severe pollution in this region, concerns have been raised by the consumers with the safety of clams they purchased or may purchase. To address these concerns, we conducted a multi-year survey to determine the levels of As and As species in five major clam species cultivated in eight production areas of this region. Based on the above analysis data, Bayesian statistics used a Markov Chain Monte Carlo approach was applied to predict the toxic As residue distributions in clams produced in this region and their health risks to Chinese adults. It was found that the bioaccumulation ability of total As (tAs) and inorganic As (iAs) was species-specific, while Mactra veneriformis (MV) had the strongest accumulation capacity for toxic iAs (0.22–2.85 mg/kg dw). Up to 6.7% of the tested MV samples exceeding the iAs limit of China Food and Drug Administration. The content of iAs was also found to be related significantly to the harvest seasons, with clam in the spawning period (June) having the lowest iAs concentrations. The non-carcinogenic and carcinogenic health risk from dietary exposure to iAs associated with MV consumption was rather high, which suggested that specific attention should be paid to the safety of clam consumption in this region.</p

Comparison of LOD values of QTL associated with SalinityD tolerance on chromosome 2H (A) and 5H (B) before and after flowering time was used as a covariate.

<p>Map distances in centiMorgan (cM) shown to the left. The vertical dotted line indicates the significance threshold of LOD 3.0. Black: LOD value range of original QTL; Green: new LOD value range of QTL when trait of flowering time was used as a covariate.</p

Table_1_Rumen and fecal microbiota profiles associated with immunity of young and adult goats.xls

Low immunity at birth increases risk of disease of young livestock, such as goat kids. Microbiomes change as animals mature, and a healthy microbiome is related to decreased risk of disease. The relationship between microbiota profiles and immunity at different developmental stages remains unclear. Young (female, n = 12, 30 d) and adult (female, n = 12, 2 yrs. old) Saanen dairy goats were used to investigate changes in rumen microbiomes, fecal microbiomes, and their correlations to circulating immune factors. Serum IgG (P = 0.02) and IgM (P < 0.01) were higher at 2 years than 30 d of age, but there were no differences in IgA (P = 0.34), IL-2 (P = 0.05), IL-4 (P = 0.37) and IL-6 (P = 0.73) between ages. Amplicon sequencing analysis revealed young goats had a higher diversity of bacterial communities in rumen and lower diversity in feces compared with adult goats. Ten genera in rumen and 14 genera in feces were positively correlated with serum IgM concentration across both ages. Olsenella, Methanosphaera, Quinella, Candidatus_Saccharimonas, and Methanobrevibacter in rumen and Ruminobacter, Treponema, Rikenelaceae_ RC9_ gut_ Group in feces were positively correlated with the concentration of IgG. The correlation analysis using weighted gene co-expression network analysis showed the MEblue module was positively associated with the IgG and IgM. These data provide novel insight into the association between rumen-feces microbiota and immune response. Further experiments are needed to investigate whether inoculating young livestock with immune-related bacteria identified can improve the immune status. Our data suggest a possible strategy to improve the immunity of the kids by alterative microbiota profiles.</p

DataSheet1_Multi-Year Survey and Bayesian Modeling Approach for Characterizing Arsenic Pollution in Marine Clams Cultivated Along the Tidal Flats of Mid-Eastern China.DOC

Marine clam is one of the main sources of arsenic (As), and the tidal flats of Jiangsu Province are considered major culturing areas for clams in mid-eastern China. In view of increasingly severe pollution in this region, concerns have been raised by the consumers with the safety of clams they purchased or may purchase. To address these concerns, we conducted a multi-year survey to determine the levels of As and As species in five major clam species cultivated in eight production areas of this region. Based on the above analysis data, Bayesian statistics used a Markov Chain Monte Carlo approach was applied to predict the toxic As residue distributions in clams produced in this region and their health risks to Chinese adults. It was found that the bioaccumulation ability of total As (tAs) and inorganic As (iAs) was species-specific, while Mactra veneriformis (MV) had the strongest accumulation capacity for toxic iAs (0.22–2.85 mg/kg dw). Up to 6.7% of the tested MV samples exceeding the iAs limit of China Food and Drug Administration. The content of iAs was also found to be related significantly to the harvest seasons, with clam in the spawning period (June) having the lowest iAs concentrations. The non-carcinogenic and carcinogenic health risk from dietary exposure to iAs associated with MV consumption was rather high, which suggested that specific attention should be paid to the safety of clam consumption in this region.</p