There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.

The present study used a combination of 16S rRNA MiSeq sequencing strategy and gas chromatograph time of flight mass spectrometer (GC-TOF/MS) technique to investigate the effects of starch sources on the colonic microbiota and their metabolites in finishing pigs. A total of 72 crossbred barrows were allocated to three different experimental diets with eight replicates and three pigs per replicate. The diet types included tapioca starch (TS), corn starch (CS), and pea starch (PS) (amylose/amylopectin were 0.11, 0.25, and 0.44, respectively). Results showed that the PS diet markedly increased (adjusted P < 0.05) the abundance of short-chain fatty acids (SCFAs) and lactate producers, such as Lactobacillus, Prevotella, Faecalibacterium, and Megasphaera, while decreased (adjusted P < 0.05) the abundance of Escherichia coli when compared with the TS diet. The metabolomic and biochemistry analyses demonstrated that the PS diet increased (adjusted P < 0.05) the concentrations of organic acids (acetate, propionate, butyrate, valerate, and lactate) and some macronutrients (sugars and long-chain fatty acids), and decreased (adjusted P < 0.05) the amino acids and their derivatives (leucine, glycine, putrescine, cadaverine, skatole, indole, and phenol) when compared with the TS diet. Additionally, Spearman's correlation analysis revealed that the changes in the colonic metabolites were associated with changes in the microbial composition. Correlatively, these findings demonstrated that the different dietary starch types treatment significantly altered the intestinal microbiota and metabolite profiles of the pigs, and dietary with higher amylose may offer potential benefits for gut health.

In modern swine husbandry systems, antibiotics have been used as growth promoters for piglets during suckling or weaning period. However, while early colonization of intestinal microbiota has been regarded crucial for the host's later life performance and well-being, little is known about the impact of antibiotics on intestinal microbiota in suckling piglets. The present study aimed to investigate the effects of early antibiotics exposure on gut microbiota and microbial metabolism of suckling piglets. Sixteen litters of suckling piglets were fed a creep feed diet with (Antibiotic) or without (Control) antibiotics from postnatal days 7-23 (n = 8). The ileal and cecal digesta were obtained for microbial composition and microbial metabolites analysis. The results showed that the antibiotics significantly altered the bacterial community composition by decreasing (P < 0.05) the diversity and richness in the ileum. The antibiotics significantly reduced the abundance of Lactobacillus in both the ileum and cecum, increased the abundance of Streptococcus, unclassified Enterococcaceae, unclassified Fusobacteriales, and Corynebacterium in the ileum, and the abundance of unclassified Ruminococcaceae and unclassified Erysipelotrichaceae in the cecum. The antibiotics decreased (P < 0.05) ileal lactate concentration and cecal concentration of total short-chain fatty acids (SCFAs). But the antibiotics enhanced protein fermentation (P < 0.05) in the ileum and cecum, as ileal concentrations of putrescine and cadaverine, and cecal concentrations of isobutyrate, isovalerate, putrescine, cadaverine, spermine, and spermidine were significantly increased (P < 0.05). These results indicated that early antibiotics exposure significantly altered the microbial composition of suckling piglets toward a vulnerable and unhealthy gut environment. The findings provide a new insight on the antibiotics impact on neonates and may provide new framework for designing alternatives to the antibiotics toward a healthy practice for suckling piglets.

The present study aimed to investigate the effects of citrus extract (CE) on intestinal microbiota, microbial metabolite profiles, and the mucosal immune status in broilers. A total of 540 one-day-old yellow-feathered broilers were randomly allotted into three groups and fed a basal diet (control group), or a basal diet containing 10 mg/kg of zinc bacitracin (antibiotic group), or 10 mg/kg of CE (CE group). Each treatment consisted of six replicates, with 30 broilers per replicate. After 63-day feeding, two broilers per replicate were randomly selected and slaughtered, and their ileal and cecal digesta and ileal tissue were collected for microbial composition, microbial metabolites, and gene expression analysis. The results showed that CE significantly increased the abundance of Barnesiella and Blautia than did the antibiotic group (adjusted P < 0.05), whereas it decreased the abundance of Alistipes and Bacteroides (adjusted P < 0.05). Meanwhile, the CE group also increased the numbers of Bifidobacterium and Lactobacillus than did the control and antibiotic groups (P < 0.05), whereas it decreased the number of Escherichia coli (P < 0.05). For microbial metabolites, dietary supplementation with CE increased the concentrations of lactate, total short-chain fatty acids, acetate, and butyrate in the cecum than did the control and antibiotic groups (P < 0.05), whereas it decreased the concentrations of amino acid fermentation products (ammonia, amines, p-cresol, and indole) (P < 0.05). Additionally, supplementation with CE up-regulated (P < 0.05) the mRNA expression of intestinal barrier genes (ZO-1 and Claudin) in the ileum than did both the control and antibiotic groups. However, antibiotic treatment induced gut microbiota dysbiosis, altered the microbial metabolism, and disturbed the innate immune homeostasis. In summary, these results provide evidence that dietary supplementation with CE can improve the intestinal barrier function by changing microbial composition and metabolites, likely toward a host-friendly gut environment. This suggests that CE may possibly act as an efficient antibiotic alternative for yellow-feathered broiler production.

Coastal ecosystems experience some of the most active land-ocean interactions in the world, and they are characterized by high primary productivity and biological diversity in the sediment. Given the roles of microorganisms in soil biogeochemical cycling and their multifaceted influence on soil ecosystems, it is critical to understand the variations and drivers of soil microbial communities across coastal ecosystems. Here, we studied soil bacterial community dynamics at different sites (from seawater to freshwater) in the Yellow River Delta, China. Bacterial community composition and diversity over four seasons were analyzed through 16S rRNA genes. Notably, the bacterial community near the ocean had the lowest alpha-diversity when compared with the other sites. No significant differences in bacterial communities among seasons were found, indicating that seasonal variation in temperature had little influence on bacterial community in the newly formed wetlands in the Yellow River Delta. Bacterial community structure changed substantially along the salinity gradient, revealing a clear ecological replacement along the gradual transformation gradient from freshwater to seawater environment. Redundancy analysis revealed that salinity was the main driver of variations in bacterial community structure and explained 17.5% of the variability. Our study provides a better understanding of spatiotemporally determined bacterial community dynamics in coastal ecosystems.

The double selection of environment adaptation and host specificity forced the diversification of rhizobia in nature. In the tropical region of China, Medicago polymorpha and Medicago lupulina are widely distributed, particularly in purple soil. However, the local distribution and diversity of rhizobia associated with these legumes has not been systematically investigated. To this end, root nodules of M. polymorpha and M. lupulina grown in purple soil at seven locations in Yunnan Province of China were collected for rhizobial isolation. The obtained rhizobia were characterized by RFLP of 16S-23S rRNA intergenic spacer, BOXAIR fingerprinting, and phylogeny of housekeeping and symbiosis genes. As result, a total of 91 rhizobial strains were classified into species Sinorhizobium medicae and S. meliloti, while three nodC gene types were identified among them. S. medicae containing nodC of type I was dominant in farmlands associated with M. polymorpha; while S. meliloti harboring nodC of type III was dominant in wild land nodulated by M. lupulina. For both rhizobial species, greater genetic diversity was detected in the populations isolated from their preferred host plant. A high level of genetic differentiation was observed between the two Sinorhizobium species, and gene flow was evident within the populations of the same species derived from different soil types, indicating that rhizobial evolution is likely associated with the soil features. To examine the effects of environmental features on rhizobial distribution, soil physicochemical traits and rhizobial genotypes were applied for constrained analysis of principle coordinates, which demonstrated that soil features like pH, nitrogen and sodium were the principle factors governing the rhizobial geographical distribution. Altogether, both S. medicae and S. meliloti strains could naturally nodulate with M. polymorpha and M. lupulina, but the rhizobium-legume symbiosis compatibility determined by both the host species and soil factors was also highlighted.

Early life is a critical window for preventing the intergenerational transmission of metabolic diseases. Betaine has been proven to play a role in improving glucose and lipid metabolism disorders in animal models. However, whether maternal betaine supplementation plays a role in regulating gut microbiota in both dams and offspring remains unclear. In this study, C57BL/6 female mice were fed with control diet (Ctr), high-fat diet (HF), and high-fat with betaine supplementation (0.3% betaine in the diet, HFB) from 3 weeks prior to mating and lasted throughout pregnancy and lactation. After weaning, the offspring got free access to normal chow diet until 20 weeks of age. We found that maternal dietary betaine supplementation significantly improved glucose and insulin resistance, as well as reduced free fatty acid (FFA) concentration in dams and offspring from young to adult. When compared to the HF group, Intestinimonas and Acetatifactor were reduced by betaine supplementation in dams; Desulfovibrio was reduced in 4-week-old offspring of the HFB group; and Lachnoclostridium was enriched in 20-week-old offspring of the HFB group. Moreover, the persistent elevated genus Romboutsia in both dams and offspring in the HFB group was reported for the first time. Overall, maternal betaine could dramatically alleviate the detrimental effects of maternal overnutrition on metabolism in both dams and offspring. The persistent alterations in gut microbiota might play critical roles in uncovering the intergenerational metabolic benefits of maternal betaine, which highlights evidence for combating generational metabolic diseases.