Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?

Background Community assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates. Aims This paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate. Results It can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.

The Temporal Dynamics of Rumen Microbiota in Early Weaned Lambs

Weaning affects the development of ruminal bacteria in lambs during early life. However, the temporal dynamics of rumen microbiota in early weaned lambs is unknown compared to conventionally weaned lambs. In this study, one group was reared with their dams (control, CON) and conventionally weaned at 49 days (d), while the other lambs were weaned at 21 d (early weaning, EW) using starter. Rumen microbial samples collected at 26, 35, and 63 d were used for next-generation sequencing. Here, we found that the abundance and diversity of rumen microbiota in EW were significantly lower at 26 and 35 d than the CON. Linear discriminant analysis Effect Size (LEfSe) analysis was performed to identify the signature microbiota for EW at these three ages. At 26 d, Prevotella 7, Syntrophococcus, Sharpea, Dialister, Pseudoscardovia, and Megasphaera in the rumen of the EW group had greater relative abundances. At 35 d, the Lachnospiraceae_NK3A20_group was enriched in CON. On 63 d, Erysipelotrichaceae_UCG-002 was abundant in EW. Syntrophococcus and Megaspheaera in EW lambs were abundant at 26 and 35 d, but kept similar to CON at 63 d. The relative abundance of Erysipelotrichaceae_UCG-002 at all-time points was consistently higher in the EW group. In conclusion, early weaning led to a significant decrease in rumen microbiota richness and diversity in the short term. The changes in rumen microbiota are associated with the persistence of weaning stress. The temporal dynamics of relative abundances of Syntrophococcus, Megasphaera, and Ruminococcaceae_UCG-014 reflect the weaning stress over a short period and rumen recovery after early weaning.

Unlike Glycerophosphocholine or Choline Chloride, Dietary Phosphatidylcholine Does Not Increase Plasma Trimethylamine-N-Oxide Levels in Sprague-Dawley Rats

Choline, betaine, and L-carnitine are transformed into trimethylamine (TMA) by gut microbiota, absorbed into the liver, and oxidized into trimethylamine-N-oxide (TMAO) by flavin-containing monooxygenases. Elevated TMAO levels may negatively affect human health. As phosphatidylcholine (PC) is the main source of dietary choline, its intake or PC-rich foods may be harmful to human health; however, quantitative comparative information among dietary choline compounds (PC, glycerophosphocholine [GPC], and choline chloride [CC]) regarding in vivo generation of TMAO is lacking. Here, we compared the effects of PC, GPC, and CC on plasma TMAO levels in rats. Furthermore, we investigated their effects on gut microbiota at the genus level. Dietary PC did not affect plasma TMAO levels, whereas dietary GPC and CC significantly increased them. At the genus level, plasma TMAO levels were significantly negatively correlated with relative abundances of Anaerotruncus, Actinomyces, Enterococcus, Dialister, Clostridium XIVa, and Granulicatella; they were significantly positively correlated with that of Coprobacter. Moreover, the relative abundances of Anaerotruncus and Coprobacter were found to predict plasma TMAO levels. Therefore, dietary PC, unlike GPC or CC, does not increase plasma TMAO levels in rats. Furthermore, several gut microbes are associated with changes in plasma TMAO levels in rats fed with choline compounds.

Effect of Bacillus amyloliquefaciens and Bacillus subtilis on fermentation, dynamics of bacterial community and their functional shifts of whole-plant corn silage

Background Bacillus amyloliquefaciens (BA) and Bacillus subtilis (BS) are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals. However, few research have reported the effects of BA and BS on fermentation characteristics and bacterial community successions of whole-plant corn silage during ensiling. If the BA and BS inoculants have positive effects on silages, then they could not only improve fermentation characteristics, but also deliver BA or BS viable cells to ruminants, which would play its probiotic effect. Therefore, the objectives of this study were to investigate the effects of BA and BS on the fermentation, chemical characteristics, bacterial community and their metabolic pathway of whole-plant corn silage. Results Freshly chopped whole-plant corn was inoculated without or with BA and BS, respectively, and ensiled for 1, 3, 7, 14 and 60 d. Results showed that BA and BS inoculations increased lactic acid concentrations of whole-plant corn silages compared with control, and BA inoculation decreased acetic acid concentrations, whereas BS inoculation decreased fiber contents and increased crude protein (CP) content. Higher water-soluble carbohydrate contents and lower starch contents were observed in BA- and BS-inoculated silages compared with that in control. The decreased CP content and increased non-protein nitrogen content were observed in BA-inoculated silage, which was consistent with the higher amino acid metabolism abundances observed in BA-inoculated silage. In addition, it was noteworthy that BA and BS inoculations increased the metabolism of cofactors and vitamins, and decreased the relative abundances of drug resistance: antimicrobial pathways. We also found that the bacterial metabolism pathways were clearly separated into three clusters based on the ensiling times of whole-plant corn silage in the present study. There were no significant differences in bacterial community compositions among the three groups during ensiling. However, BA and BS inoculations decreased the relative abundances of undesirable bacteria such as Acetobacter and Acinetobacter. Conclusion Our findings suggested that the BS strain was more suitable as silage inoculants than the BA strain in whole-plant corn silage in this study.

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates

Patterns of sequencing coverage along a bacterial genome---summarized by a peak-to-trough ratio (PTR)---have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce CoPTR (Compute PTR): a tool for computing PTRs from complete reference genomes and assemblies. Using simulations and data from growth experiments in simple and complex communities, we show that CoPTR is more accurate than the current state-of-the-art, while also providing more PTR estimates overall. We further develop theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with inflammatory bowel disease. We show that growth rates are personalized, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by demonstrating how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.

Volatile Abundances, Extended Coma Sources, and Nucleus Ice Associations in Comet C/2014 Q2 (Lovejoy)

High-resolution infrared spectra of comet C/2014 Q2 Lovejoy were acquired with NIRSPEC at the W. M. Keck Observatory on two post-perihelion dates (UT 2015 February 2 and 3). H2O was measured simultaneously with CO, CH3OH, H2CO, CH4, C2H6, C2H4, C2H2, HCN, and NH3 on both dates, and rotational temperatures, production rates, relative abundances, H2O ortho-to-para ratios, and spatial distributions in the coma were determined. The first detection of C2H4 in a comet from ground-based observations is reported. Abundances relative to H2O for all species were found to be in the typical range compared with values for other comets in the overall population to date. There is evidence of variability in rotational temperatures and production rates on timescales that are small compared with the rotational period of the comet. Spatial distributions of volatiles in the coma suggest complex outgassing behavior. CH3OH, HCN, C2H6, and CH4 spatial distributions in the coma are consistent with direct release from associated ices in the nucleus and are peaked in a more sunward direction compared with co-measured dust. H2O spatial profiles are clearly distinct from these other four species, likely due to a sizable coma contribution from icy grain sublimation. Spatial distributions for C2H2, H2CO, and NH3 suggest substantial contributions from extended coma sources, providing further evidence for distinct origins and associations for these species in comets. CO shows a different spatial distribution compared with other volatiles, consistent with jet activity from discrete nucleus ice sources.

Supplementing Glycerol to Inoculum Induces Changes in pH, SCFA Profiles and Microbiota Composition in In-Vitro Batch Fermentation

Glycerol was generally added to the inoculum as a cryoprotectant. However, it was also a suitable substrate for microbial fermentation, which may produce more SCFAs, thereby decreased pH of the fermentation broth. This study investigated the effect of supplementing glycerol to inoculum on in vitro fermentation and whether an enhanced buffer capacity of medium could maintain the pH stability during in vitro batch fermentation, subsequently improving the accuracy of short chain fatty acids (SCFAs) determination, especially propionate. Two ileal digesta were fermented by pig fecal inoculum with or without glycerol (served as anti-frozen inoculum or frozen inoculum) in standard buffer or enhanced buffer solution (served as normal or modified medium). Along with the fermentation, adding glycerol decreased the pH of fermentation broth (p < 0.05). However, modified medium could alleviate the pH decrement compared with normal medium (p < 0.05). The concentration of total propionic acid production was much higher than that of other SCFAs in anti-frozen inoculum fermentation at 24 and 36 h, thereby increasing the variation (SD) of net production of propionate. The α-diversity analysis showed that adding glycerol decreased Chao1 and Shannon index under normal medium fermentation (p < 0.05) compared to modified medium (p < 0.05) along with fermentation. PCoA showed that all groups were clustered differently (p < 0.01). Adding glycerol improved the relative abundances of Firmicutes, Anaerovibrio, unclassified_f_Selenomonadaceae, and decreased the relative abundance of Proteobacteria (p < 0.05). The relative abundances of Firmicutes, such as Lactobacillus, Blautia and Eubacterium_Ruminantium_group in modified medium with frozen inoculum fermentation were higher than (p < 0.05) those in normal medium at 36 h of incubation. These results showed that adding glycerol in inoculum changed the fermentation patterns, regardless of substrate and medium, and suggested fermentation using frozen inoculum with modified medium could maintain stability of pH, improve the accuracy of SCFA determination, as well as maintain a balanced microbial community.

Altered intestinal microbiota are associated with sleep disturbances in patients with minimal hepatic encephalopathy caused by hepatitis B-related liver cirrhosis

Objective Minimal hepatic encephalopathy (MHE) caused by liver cirrhosis is quite prevalent, and approximately one-half of MHE patients have experience sleep disturbances. This study systematically evaluated the association between sleep disturbances and altered intestinal microbiota in patients with MHE caused by hepatitis B-related liver cirrhosis. Methods Ninety-eight and 45 MHE patients were respectively included in the exploration and validation cohorts. The Chinese version of the Pittsburgh Sleep Quality Index (PSQI) questionnaire was used to evaluate sleep disturbances. The intestinal microbiota of self-collected fecal samples was analyzed using the amplicon sequencing of bacterial 16S ribosomal RNA gene. Results MHE patients with sleep disturbances were characterized by lower bacterial diversities and distinct microbial composition in comparison to those without sleep disturbances. The relative abundances of Salivarius, Veillonella, Klebsiella, and Eubacterium were independent predictors of sleep disturbances in MHE patients. In MHE patients with sleep disturbances, the relative abundances of Salivarius and Veillonella were positively correlated with PSQI scores, respectively. Functional modules involved in lipopolysaccharide biosynthesis, as well as protein digestion and absorption, were increased in the microbiome of MHE patients with sleep disturbances. Conclusion Salivarius and Veillonella may be potential diagnostic biomarkers and therapeutic targets for sleep disturbances in MHE patients.

Reintroduction of Decomposed Straw To Maize Fields Resulted In Soil Microbial Community Change And Increased Corn Production

Purpose Returning decomposed straw to crop fields could address many agricultural shortcomings. In this study, the soil microbial community, soil nutrients, soil enzyme activities and maize yield were investigated after returning decomposed straw to the field. Methods To investigate the effects of returning decomposed straw to field on soil microorganisms and maize growth, field experiments were carried out to measure soil nutrient content, soil enzyme activity and maize yield, and the soil microbial community structure was measured by 16SRNA and ITS amplicon sequencing technology.Results The results showed that the contents of total nitrogen (TN), nitrate nitrogen (NN), total phosphorus (TP), available phosphorus (AP) and pH were significantly increased, and the contents of ammonium nitrogen (AN) and available kalium were decreased in both the rotary tillage (SR) and mulching (SM) treatments. The bacterial and fungal community structures in bulk and rhizosphere soils were clearly changed under SR and SM. The relative abundances of bacterial genera related to soil denitrification, such as Skermanella, Blastococcus, Geodermatophilus and Asanoa, were significantly increased. The relative abundances of Conexibacter, Streptomyces and Trichoderma, which bacteria that has shown to inhibit plant diseases, were increased. In addition, the relative abundances of growth-promoting bacteria, such as Arthrobacter and Mesorhizobium, were also significantly increased. Moreover, adding decomposed straw back to the field promoted the absorption of nutrients by maize, and resulted in higher yield of maize.Conclusions Our findings suggest positive responses of soil microbial community structure and maize growth to decomposition straw returning.

Dietary Quercetin Supplementation Attenuates Diarrhea and Intestinal Damage by Regulating Gut Microbiota in Weanling Piglets

Antioxidant polyphenols from plants are potential dietary supplementation to alleviate early weaning-induced intestinal disorders in piglets. Recent evidences showed polyphenol quercetin could reshape gut microbiota when it functioned as anti-inflammation or antioxidation agents in rodent models. However, the effect of dietary quercetin supplementation on intestinal disorders and gut microbiota of weanling piglets, along with the role of gut microbiota in this effect, both remain unclear. Here, we determined the quercetin’s effect on attenuating diarrhea, intestinal damage, and redox imbalance, as well as the role of gut microbiota by transferring the quercetin-treated fecal microbiota to the recipient piglets. The results showed that dietary quercetin supplementation decreased piglets’ fecal scores improved intestinal damage by increasing tight junction protein occludin, villus height, and villus height/crypt depth ratio but decreased crypt depth and intestinal epithelial apoptosis (TUNEL staining). Quercetin also increased antioxidant capacity indices, including total antioxidant capacity, catalase, and glutathione/oxidized glutathione disulfide but decreased oxidative metabolite malondialdehyde in the jejunum tissue. Fecal microbiota transplantation (FMT) from quercetin-treated piglets had comparable effects on improving intestinal damage and antioxidative capacity than dietary quercetin supplementation. Further analysis of gut microbiota using 16S rDNA sequencing showed that dietary quercetin supplementation or FMT shifted the structure and increased the diversity of gut microbiota. Especially, anaerobic trait and carbohydrate metabolism functions of gut microbiota were enriched after dietary quercetin supplementation and FMT, which may owe to the increased antioxidative capacity of intestine. Quercetin increased the relative abundances of Fibrobacteres, Akkermansia muciniphila, Clostridium butyricum, Clostridium celatum, and Prevotella copri but decreased the relative abundances of Proteobacteria, Lactobacillus coleohominis, and Ruminococcus bromii. Besides, quercetin-shifted bacteria and carbohydrate metabolites short chain fatty acids were significantly related to the indices of antioxidant capacity and intestinal integrity. Overall, dietary quercetin supplementation attenuated diarrhea and intestinal damage by enhancing the antioxidant capacity and regulating gut microbial structure and metabolism in piglets.